Coccidia and the Healthy Dog

What is coccidia and how do dogs and puppies acquire this illness?

Coccidia is a disgusting little protozoa. This single-celled organism travels to the host animal’s intestines after being ingested and sets up shop.

Coccidia affects many species of animal, including humans! Thankfully, the genus and species of coccidia that affect each species of animal is a different variety of coccidia entirely. So your pet birds often won’t give the dog their cocci and your dogs are very unlikely to share cocci infections with your children.

There are genus and species that share with each other (sharing is caring!) and so wild animals can bring this nasty thing into your yard to infect your pets.

However, immunocompromised people are more susceptible to a particular type of coccidia that dogs can have called cryptosporidium. Fortunately, this type of cocci is more rare in dogs. Most dogs are infected with the genus called isospora, and typically only one species within that genus.

So hurray for that!!

Toxoplasmosis is one type of coccidia infection that lives in cats. Felines are the normal host reservoir for this dangerous protozoa and one reason why I really detest my neighbors that allow their cats to run wild all over the neighborhood (and my property).

Toxoplasmosis will cross a placenta and injure or kill baby creatures growing therein, to include puppies and human babies. This is also a nasty infection that will make both adult humans and dogs rather ill and will very quickly kill a litter of newborn puppies. I’m crossing my fingers that I never run into this one but fortunately it is pretty rare in dogs.

The dog-common genus of cocci parasite is called isospora and is not typically very dangerous for puppies but it is rather difficult to get rid of once it sets up shop on a property. It is sometimes called “raccoon fever” as one main host reservoir species in the wild raccoon. So there ya go. Racoon poop. It’s not all it’s cracked up to be.

How does a dog or puppy get infected?

Dogs become infected with this parasite by eating disgusting, dead animals or by eating the poop of infected animals. Rule number one for avoiding illness is always “don’t eat poo”. I joke but really it is so true. Poo eating results in illness. Avoid doing it and don’t allow your canine pal to do it either. Poo… is not ‘what’s for dinner’!

One really good way to avoid your dog eating poop or dead animals is to remove all poop that you find on your property. The same can be said for dead animals. Keep carrion and poop out of your yard and walkways. This seems like a “duh” but believe me, I’ve seen it, people let gross happen and never underestimate the power of lazy in people.

To be fair, some people live in rural areas, and then it can be impossible to find all the lovely poo or dead animals that your dog’s amazing nose will quickly ferret out.

Another good way to prevent poo or carrion-eating in dogs is to ensure your dog is well fed (and not half starved) and is being fed a really high-quality, high-protein diet. Many kibbles are very low in quality (even if the bag tells you otherwise) and dogs may feel the need to eat poop to get nutrients they are missing. I also think that it says something to the quality of flavor of your dog food in your dog is voluntarily eating crap 😉

Coprophagia (or the eating of one’s own poop) is a very undesirable and dangerous behavior for dogs (well probably for any pet, other than rabbits who need to eat their own poop to be healthy). To learn more about it click the link. This is a nasty problem that can occur in dogs that are fed well and otherwise healthy, so if your dog has this problem don’t beat yourself up and click the link for ways to help understand and manage this nasty habit.

Coccidia does not pass from an infected mother to her young via milk like roundworms or across the little placentas that filter all the blood supply to tiny developing pups. So how do puppies acquire this illness? They have to come in contact with and consume some of an infected dog’s poo. (Remember that first rule?)

You will see coccidia present in the litters of well kept puppies as well as in poorly bred and kept litters.

In poorly maintained litters you will see this crop up nearly 100% of the time. This is because the whelping areas and the dams are not cleaned very often at all and when they are, the cleaning is not very thorough.

Alas, coccidia can also worm its way into the tummies of well-kept, very clean litters as well. Which is very annoying.


My mother dogs are house-trained and my mother dogs are allowed free access to their puppies and may come and go into the whelping/nursery area as they please (they are not trapped in a locked wire crate or cage with their puppies because I think that is horrible). My girls are not ever eliminating their waste (poop or pee) anywhere remotely near their babies as they are not forced to and their urge not to do so is incredibly strong. So how the heck did my puppies pop up with this illness?

For starters I begin outdoor house training of puppies at about 4 weeks of age (weather permitting). Even though I pick up adult poop relatively quickly (often immediately) the nasty little protozoa shed their eggs and they can live in moist grass, dirt and even well-cleaned gravel for up to 2 years! So if the puppies romped through any area where an infected dog pooped previously, even though it is cleaned up, the puppies’ feet could pick up an isospora oocyte (fancy words that mean protozoan egg). Puppies later groom themselves and one another as well as step all over each other and often into their food and water dishes at feeding time as well.

Mom might also walk through her own poop after “going”. (Hey give mom a break! She may have just whelped 8 babies! If I gave birth to 8 babies at once I’d be happy if I could get up to go poop all by myself at all. Ha!)

So if mom steps in it and then walks back into her box even the most microscopic (and therefore not visible or smell-able by me) bit of poop can get in and infect one or several of her puppies.

These eggs are also very sticky (and microscopic) and easily stick to the fur on mom’s rear end, tail and legs.

Dogs that go to dog shows, kennels to board, events, fairs, beaches, dog parks or even just going to the veterinarian can pick up this nasty little protozoa on their paws, rear and belly and later groom themselves and acquire the infection.


Oh, poo. It’s a coccidia infection. No, literally. Poo. Coccidia can cause nasty foul-smelling diarrhea in puppies. Can. Doesn’t mean that it will. So a sneaky infection can be present without anyone detecting its presence.

Coccidia can present with soft-pudding like puppy poop, foul-smelling or strong-smelling poop, and even vomiting or explosive, watery diarrhea. Or, as often is the case, no symptoms may be present at all.

Puppies often have soft stool as they are weaning and making the transition from milk to dog food so it is very easy to miss an infection and often mama dogs have loose or off stool from changing hormone levels, cleaning up after puppies because I wasn’t fast enough, eating too much afterbirth or just about anything you can think of. So therefore it is incredibly easy to mistake coccidia infection symptoms with normal new-puppy or new-mama adjustments, to include soft poop from a stressed puppy that just came home with you.

In healthy, fat, well-fed and well-bred puppies these common puppy parasites pose very little health risk. Many puppies that have coccidia are never even diagnosed as often the eggs aren’t present in the small sampling of stool at the vet even if the pup has the parasite (this is true for all “worms” too!) The main concern with infection is dehydration due to diarrhea. A long lasting infection can cause anemia but coccidia is typically fairly mild and not of much concern. Especially in puppies that are already very healthy and well raised.

Most puppies simply “outgrow” the infection. Their bodies become mature and strong enough to fight off the infection successfully. They keep the infection at bay, so to speak. But the protozoa still inhabits the dog’s digestive tract. And as a result an otherwise healthy dog becomes a “carrier” of the disease and sheds viable oocytes (eggs) everywhere they poop. Even if their poop is immediately cleaned up it contaminates the soil and waits for its next hapless victim. And then in times of stress, illness or other poor health the coccidia infection (which is still there) blooms and causes an active, nasty infection in your poor dog that seemed otherwise quite parasite-free.

This is why you see/read puppy-sellers telling you that stress can “cause” parasite blooms and watery diarrhea in dogs and puppies. You see, while stress can cause severe diarrhea (especially in really nervous, anxious or poorly socialized puppies) it is a whole lot more likely that the severe diarrhea is being caused by a parasite getting a good bloom in due to a stressed out puppy or dog.

Even for a well socialized puppy, travel to a new home and just transitioning to a new home causes stress and can cause a little bit of diarrhea and/or vomiting. But there is a big difference between one or two bouts of soft poop and persistent, watery diarrhea. So don’t be fooled.

Regardless of where you get your new puppy, you should always see a vet right away and have a stool sample taken to check for common puppy parasites (because they are just so hard to avoid in new puppies). Better to be safe, get checked and treated, than to believe it’s “just stress” and potentially leave parasites untreated.

Stress doesn’t “cause” coccidia as many puppy-hawkers claim. Coccidia causes coccidia infections. Stress just makes the immune system lower and already present infections take advantage of that because that is what infectious organisms do. They kick you when you’re down and free-load.

If you can’t tell by now I really hate parasites. They are disgusting and really hard to eradicate. But it is what it is, they exist in the world and you cannot avoid them! Every breeder and pet owner must have a good plan set up with trusted veterinarians to keep these little jerks out of your dog’s system.

This is most especially important for young or old dogs and for dogs that visit immunocompromised human beings. Since we work with dogs that visit hospitals on a regular basis, this has been an important part of our program.

It’s not about “winning the battle” against Mother Nature. It’s all about regular health care and maintenance of a quality program that works properly. Which is no easy task!


Coccidia (isospora) is treated by your local vet with an antibiotic, usually one called Albon. Coccidia isn’t a bacterial infection so why treatment with an antibiotic, you ask? Well the Albon is what is called a sulfa-drug and it messes up the reproduction ability of single-celled organisms like bacteria and coccidia by preventing folic acid use (or something science-y like that). After screwing up the RNA in these little buggers they are unable to reproduce and therefore cannot continue their life-cycle in their host (your adorable dog).

Now that doesn’t actually kill the protozoa or the protozoan eggs that are present in your dog or in your dog’s immediate environment (wherever your dog may have shed or tracked ooctyes). It just neuters them, so to speak. Just the ones currently living in the dog.

These damaged Protozoa are eventually killed by the immune system of the dog or passed in the poop or die of their own accord and the infection clears up as these Protozoa have been unable to reproduce.

Because the protozoa have to die off, medication treatment is a long time (relatively speaking). It takes about 10 days and in some (often severe) cases there needs to be re-treatment in 2 weeks’ time since the environment is often contaminated by viable eggs and the dog is likely to reinfect himself.

The treatment with Albon does seem to reduce symptoms like diarrhea however, and certainly shortens the normal length of time there is an infection present. If you treat with Albon (vs not treating at all) you have a far lower risk of your dog being a host carrier of the nasty parasite and having flare-ups or “blooms” later in life. So if you’ve got cocci please have it treated.

Alternative Medicine

There are no proven holistic or alternative or “natural” methods or drugs or herbal remedies available that have any worthwhile effect on coccidia (and most other puppy parasites). I am truly all for natural treatment and I really avoid chemicals where and how I can in my kids and dogs, but this is one of those areas where you really just have to treat (or treat to prevent) with medication.

Some strains of coccidia are thought to be resistant to Albon (which is a bad thing of course) so why isn’t there some other medication that can actually kill the darn parasite?

There is. It is called “Baycox” by Bayer (toltrazuril), but it is off-label use in the United States for puppies and kittens. It is used in the US for animals like piglets, horses, cattle and chickens, however. And large animal vets regularly prescribe it off-label for professionals working with companion animals. But your common companion animal veterinarian often hasn’t even heard of the drug.

This is a drug that is very commonly used for companion animals in other first world countries, so why we have to deal with slow, expensive antibiotic treatments like Albon, I really don’t know. It’s definitely an FDA and money thing. But I try not to question the pharmaceutical industry too much, because it boils down to a money and politics thing, and not a “what is good for medical treatment” thing. That is the way of the corporate giants, unfortunately.

Baycox (toltrazuril) is available for over-the-counter sale in Australia and Canada and also breeders are able to purchase from American vets that will prescribe the medication and are familiar with its “off label” use in companion animals.

Baycox kills all life stages of coccidia but it cannot penetrate an actual egg. Therefore it is best to treat once very early (in the first 13 days after initial exposure to cocci) in order to completely eradicate it before it has any chance to produce nasty little lingering eggs.

If the coccidia isn’t caught until after oocytes are present then simply treat with the correct dosage of Baycox and then in 13 days treat again with the correct dosage of Baycox. Voila. Parasite destroyed. Protozoa: 0; Dog and Master: 1.

It is important to use the Baycox formulated for piglets. There is another that is formulated for chickens and other poultry and is meant to be added to water.

Dog and cat owners use the piglet solution. Some small animal veterinarians will prescribe off-label use of the drug to pet owners but many veterinarians only see pet owners and not pet professionals and therefore may not have any clue whatsoever what the hell ‘Baycox’ even is at all.

So if you see Baycox (toltrazuril) on the health record of a puppy be prepared for the vet to give you the one-eyebrow-up at your wellness exam. It is becoming more well-known to small animal vets as the majority of high-quality companion animal professionals are now using this medication as a preventative. So it is catching on.

So there you have it; extremely expensive imported Australian medication made by Bayer (an American company) that is really useful and safe for treating all kinds of nasty coccidian infections and is the drug of choice for puppy breeders and dog owners, exhibitors, trainers and other professionals.

Ponazuril is now available over-the-counter in the US in a horse-paste formulation and works similar to toltrazuril, however it is very hard to accurately dose in the horse paste form and unless you have a very large dog, I do not recommend using this preparation.

Albon is less effective but readily available at your local veterinarian and requires consistent dosage and often repeated dosage, but stay on top of that and your dog will conquer the cocci infection and hopefully build up a good, strong immune system that will beat it off the next time it comes a-callin’.

Symptom Management

If you have diarrhea in a dog you can feed your dog puréed pumpkin (the type you find in a can at the grocery store) or mashed sweet potatoes. There are also pumpkin supplements available at pet stores for a fortune that do the same thing. You can also purchase dog food that contain these ingredients to help firm up loose stool. This is a very safe and natural way to manage diarrhea symptoms in dogs of all ages.

Managing Contamination

Environmental contamination is a big thing to consider. Unfortunately, coccidia doesn’t like to die. Research shows that you pretty much need a flamethrower to kill these little bastards.

Some studies show that a 10% ammonia solution may kill some of the cysts in the environment, but honestly, the best thing you can do is wash all dog bedding and toys in a good, hot washing machine and then cook them on a long drying cycle. Dishes should be run through a very hot dishwasher. The yard can be scorched by that flamethrower (haha) but no commercial cleaner will do the trick on porous surfaces.

Pick up poop right away and you can hope for a heavy rain and a ton of sunlight to eventually destroy the eggs outside. There really isn’t anything else you can do.

You can use soap and water to clean hard surfaces indoors to mechanically remove cysts. But there is little else you can do, here, as well.

I also recommend giving your dog a really good bath midway through medication treatment and again following treatment to mechanically remove eggs from the coat. There is no medicated shampoo that will do the trick. So use a good sudsy soap and loads of rinsing water to rinse them down the drain.

And remember guys; Rule number one: Don’t Eat Poo!

**And of course here I have to state and use the disclaimer that you expect to see: I am not a veterinarian and this article is for information purposes only and is not meant to diagnose, treat or cure any animal or human of any possible type of condition. If you suspect your dog, child, hamster or grandma may have an illness please consult with the proper professional for the job with a proper PhD (and insurance policy) who can see your animal in person and examine your animal’s poop under a microscope.

I am not the proper professional for the job, nor do I claim to be. So if anyone kills or injures their dog (or grandma) by properly or improperly applying anything they have read herein it is completely not my responsibility (please do not sue me).

Thank you for taking the time to read my disclaimer. If you’re on this page then you read this disclaimer. Capiche? 😉 I live in NJ and I’m Italian so I totally get to say that, right?**

3 thoughts on “Coccidia and the Healthy Dog

  1. You will see coccidia present in poorly bred and kept puppy litters nearly 100% of the time. This is because the litter boxes and the dams are not cleaned very often at all and when they are the cleaning is not very thourough. …..
    This is a terrible thing to say!
    Our puppies pens are cleaned twice a day, as is the outside terracota tiled puppy area… we are so clean that I often wonder if we are too clean! …. but we have 9 week old litter that have Coccidia.
    Damning breeders in this way is not helpful .

    • I’m not sure how you misunderstood, because directly below that line I talked about how clean my litters are and all the ways excellent breeders also get this parasite.

      I’m sorry for the confusion, I will edit the post so as to clarify.

      I posted this because I see coccidia as well, it is really easy to get this on your property and in your puppies. I really feel badly that you misunderstood what I was saying!

      I am a breeder and you’re right in feeling frustrated at how often we are condemned, so I will fix that line to say that while you’ll see it in unclean litters nearly 100% of the time, you’ll also still see it pop up in really well cared for litters.

      My advice to you is to use Baycox (toltrazuril) by Bayer in your adult dogs and in your puppies.

      If you use this medication correctly (and it’s so simple and safe for puppies and kittens) you won’t see this very annoying Protozoa anymore!

      Good breeders fret a lot about parasites, it’s why I wrote the article, to talk about how easy they are to have and how frustrating they are and that it *isn’t* a sign of an unclean environment!

      I genuinely apologize that my post was confusing in this way, as that is not at all my intent.

      Thank you for your feedback so that I can correct the confusion!

    • Also, I personally clean closer to 6 times a day with puppy pens. Twice a day would not suffice for my set up, but I realize this is completely dependent upon your particular set up.

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