Common Reasons and Tips for Puppy Diarrhea

Below is a video of us discussing some of the most common reasons for diarrhea:

The one common issue with puppies is that they can have very sensitive stomachs. So many things can cause diarrhea, loss of appetite, vomiting, etc… We are always struggling to figure out what is causing what for each puppy. You definitely want to and need to stay on top of it. It can get bad very quick especially if he doesn’t eat or drink and/or vomits. The most common causes recently are:

  1. Stress– This is the most common reason why pups that go home get diarrhea. We never truly believed stress caused diarrhea until experience taught us the hard way. We learned by experience that when a pup travels long distances (8+ hours) that about 50% of them got diarrhea. We found that younger pups especially were prone to getting diarrhea in the first week of going home. Nothing was changed with food and water, yet they still would get diarrhea. Stress causes diarrhea more than any other reason in pups going home. We try to prevent “stress diarrhea” by giving our pups anti-diarrhea medicine before going home and providing you with Pro-pectalin, metronidazole and Forti-flora. This is mainly to keep your pups stool firm when traveling and adjusting to their new home.
  2. Giardia– Closely behind stress, giardia is another cause of diarrhea in puppies. The biggest reason is that there is  no medicine that truly kills it permanently. It’s very contagious passing through fecal matter and it lives in almost any kennel that’s been established for a few years. There are a couple of medicines that can suppress it enough for his immune system to overcome it. Panacur (fenbendazole) & Flagyl (metronidazole) are the best medicines for it that we have found. A 10 day treatment of both together is the best combination. If your pup has diarrhea and your vet tests for giardia, make sure to have them test for active giardia and not antigen giardia. That is where they test to see is there is ova or giardia cyst in their fecal. Sending off to an outside lab like IDEXX is the most reliable way. Most of our pups will test positive for giardia antigen which basically means your pup had diarrhea in the past. Only treat your pup if they have active giardia. The reason is that they could develop a resistant strand of giardia. We have tried everything imaginable to get rid of giardia and one of the things we tried years ago was giving many days of “preventative” treatment of panacur and flagyl. What we found was that our pups still had giardia and a very strong strand that wouldn’t be killed easier. That basically meant a pup would continue to have soft stools until they got older and their immune system beat giardia down. So only treat if you have too.
  3. Food Sensitivities/Allergies– Puppies can have sensitivities to certain foods and there is no food out there that works for every pup. TLC Whole Life Puppy Food is one of the best to work with most pups but sometimes our clients need to switch because of continual diarrhea. Simple is better. The 2 foods that our clients have used with stomach sensitivities are Canidae Grain-free Pure Sea w/ Salmon or a prescription food Royal Canin Hypoallergenic/Hydrolyzed Protein kibble. Both have worked very well. Allergies – Puppies can have allergies just like we do. We’ve had pups with the oddest of allergies before. We’ve seen pups have allergies to chicken, to grass, to barley, to Pork, to Soybean, to White Potato, to Green Peas and more. You may need to go to your vet and order an allergy test like the one found on to pinpoint the issue.
  4. Coccidia– This is another common organism found in pups. We treat them with Marquis and it does work. Unfortunately, they could have some small amount of coccidia still in them (or their littermates) that regrows after some time. If that’s the case then you vet should see this with a normal fecal and prescribe Marquis or Albon with metronidazole.
  5. Worms– We do deworm our pups every 2 weeks with a variety of dewormers but sometimes again they get through. We even check them before going home but they can have an egg that’s resistant to the dewormer hatch and spread. The most common worms are hookworm and roundworm. Panacur is one of the most popular dewormers to use even though every vet has their own favorite medicine.
  6. Bacterial Infections– This is the most complicated problem because there are so many bacterias out there. Salmonella, Ecoli, Camylobacter jejun and other issues can cause diarrhea. Medicines given vary not only on the bacteria but the specific strain of bacteria. When we have a diarrhea problem that’s not giardia, coccidia, worms or food sensitivities it’s normally some sort of bacteria infection. We then have to send off a fecal to the vet and have it tested for everything. It’s expensive but it’s really the only thing we have found to tell us exactly what we are dealing with. Depending on what the pup tests positive for is how we treat it. Anti-biotics like clavamox, doxycycline, and even baytril needs to be used sometimes to get over some of these frustrating issues.

Getting Rid of Diarrhea

Here are our suggestions:

  1. Unsweeten Pumpkin– Add a scoop of canned unsweetened pumpkin. It’s high in fiber, good tasting and great in helping diarrhea. OR you can buy Pumpkin supplement like this:
  2. Probiotics– Buy some Forti-Flora Pro-biotics and put a packet it on your pup’s food daily. By the way, you should never give panacur especially without giving pro-biotic. Many vets and pet stores have Forti-flora or you can buy it online on Amazon:
  3. Diagel– Give a dosage of Dia-Gel for dogs. It’s the best anti-diarrhea medicine that works quickly for us:
  4. Flagyl/aka Metronidazole– we give you this in your puppy packet but you probably got this from your vet as well.

There are many anti-diarrhea medicines out on the market. Every dog is different and so some medicines work better for one dog than another. We have seen no 1 anti-diarrhea medicine work for all. If nothing works then we have found it typically can be allergy related. We recommend consulting with your vet with those potential concerns.

Here are some other good anti-diarrhea medicines we recommend:

  1. Tylan Powder– is a good anti-diarrhea medicine and it helps with tear stains! This is a prescription medication.
  2. Kaolinpectin (
  3. Pro-pectalin (
  4. Immodium AD– Yep…the same stuff you give a person.


Watery diarrhea combined with vomiting could be serious. If your pup is extremely lethargic then you need to get water and energy in your pup right away. We recommend giving Dyne High Calorie Solution or Nutra-Gel as an energy supplement if your pups getting dehydrated or hypoglycemic. Seek help from your veterinarian! Pups under 6 months of age can be susceptible to quick death. 6-10 week of age is the most dangerous period. Then it’s 10-16 weeks. After 16 weeks its very rare that the pups are in danger of death but any pups under that age, be very, very watchful!