The Importance of Equine Fecal Egg Counts

Today, most horse owners hardly even think about deworming their horses. They buy a tube of whatever dewormer they think is best at the farm supply store or online, then they give it two to four times a year, usually without rhyme or reason. You might remember to give a dewormer in the fall that has potency against tapeworms. You might even think you are changing “classes” of drugs during the year. You know that’s important, but maybe you don’t even realize why you do that.

Ten, 20, or even 30 years ago, that might have been the best science for deworming horses. Early in the lifespan of oral paste dewormers, you might have given that paste every six to eight weeks (you reminded yourself of this because that’s when the farrier came). Forty to 50 years ago, some of us still remember that we had the vet out to “drench” our horses with a nasogastric tube to rid them of internal parasites. At the time, that was the best science.

A lot has changed in the past 50 years in how we treat horses to reduce the number of internal parasites. The introduction of fecal egg counts has changed how horse owners can manage internal parasites in horses.1

What hasn’t changed is that burdens of internal parasites can still make horses sick if those parasites aren’t addressed. A horse’s immune system can help keep internal parasites in check. However, not all horses’ immune systems can keep the parasites at low enough numbers so they aren’t compromising the horse’s health. This means some horses in a herd will have a larger parasite burden and be shedding more parasites into the environment than other horses. These “heavy shedders” need to be treated differently than other horses in the herd.

In this article, we’re going to talk about the changing in our understanding of internal parasite importance, resistance, and tips on deworming your horses. We’ll let you know which parasites to look out for, and how to use fecal egg counts not only to test for parasites, but to know whether your deworming program is working.

Equine Parasite Importance

The most important internal parasite for horse owners to be aware of used to be large strongyles (Strongylus vulgaris), also known as blood worms. These large strongyles were the reason horse owners used to deworm every six to eight weeks, because that matched up with the life cycle of large strongyles.

Large strongyles are small enough to travel through a horse’s arteries. This causes damage that can lead to blood clots that can detach. A heavy parasite load of large strongyles can result in anemia, diarrhea, weight loss, poor performance, and can affect growth.

As a result of modern dewormers (anthelmintics), large strongyles have been kept in check and are no longer a major threat to horse health. The same can’t be said for small strongyles (cyathostomins). Small strongyles are the most important internal parasite to be aware of today.

The larvae of small strongyles burrow into the wall of the horse’s large colon and become “encysted” to develop into the next stage of their life cycle. While they are encysted, not all dewormers can kill them.2 The dewormers that are considered effective for encysted small strongyles are moxidectin (single dose) and fenbendazole (10 mg/kg/day, daily for 5 days).4

When a large number of the larvae “excyst,” or come out of that encysted larval stage, they can cause watery diarrhea, dehydration, colic signs, and weight loss, among other issues.3 This occurs most frequently in horses less than 5 years old. Those horses can harbor hundreds of thousands of encysted small strongyle larvae.3

Then, there are pinworms (especially important to be aware of in young horses), bots, and tapeworms to consider. These are not found on fecal egg counts.

Fecal Egg Counts for Horses

Because it has been decades since a new class of dewormer has been discovered, some equine internal parasites are becoming resistant to available anthelmintics. This means when you deworm a horse, you don’t know if you are killing enough of the parasites to make a difference in the health of the horse.

Fecal egg counts are a tool that veterinarians (and educated horse owners) can use to see which parasites are present in the horse. This is done by counting the number of eggs from a fecal sample. This is generally done in the spring and fall.

You can find specifics on how to perform a fecal egg count on horses from the University of Rhode Island and Virginia Tech.5 Basically, a specific amount of fresh horse feces is taken, diluted, and a sample of the flotation material that contains parasite eggs is taken. Then, a microscope is used to identify and count the eggs. There is new automated fecal egg count equipment that your veterinarian might use to speed up the process of manually counting the eggs.

A fecal egg count also lets you identify any horse with a lot of parasite eggs in its manure. That horse is considered a “high shedder” and is spreading a lot of parasites to other horses in the herd.

The benefits of doing a fecal egg counts include:

  • You can tell which horses are shedding the most parasites in your herd.
  • It allows you to target those “high shedders” for a different deworming program.
  • It lets you deworm low shedders fewer times per year and target for specific internal parasites.

Keep in mind that not all fecal egg counts find tapeworm eggs reliably. The McMaster fecal egg count technique can miss more than 90% of tapeworm-infected horses. Your veterinarian can use other tests to reliably check on tapeworm infestations.

Fecal Egg Count Reduction Test

You also can conduct a fecal egg count reduction test. This is important information to know if the dewormer you are using is actually working.

If targeted parasite worm eggs are not reduced by a specific percentage in a specific amount of time, then the anthelmintic used is considered to be ineffective and the parasites “resistant” to that dewormer.

That means that you are spending the time and money on deworming, but not enough of the parasites are dying to make a difference in the population that is living in your horse.

Environmental Parasite Control

In addition to your deworming program that is guided by a fecal egg count, you also need to address management tools to reduce internal parasite spread.

These can include:

  • Remove manure from paddocks, dry lots, sheds, stalls, and other shared areas routinely.
  • Compost manure properly to kill parasite eggs in the manure pile.
  • Feed horses in containers to avoid contaminating foodstuffs with manure on the ground.
  • Keep shared water sources clean.
  • Spread manure piles in hot (90°F or hotter), dry weather to expose and kill parasite eggs. Note that dragging pastures when it is warm and moist can actually spread parasite eggs that can survive and infect another horse. Most parasites are not killed by cold weather, so dragging in winter just spreads the parasites throughout the field.
  • Don’t overgraze pastures.
  • Rotate horses and another species (such as cattle, sheep, or goats). Most parasites are species-specific so the life cycle can be broken.
  • Remove bot eggs from a horse’s haircoat to prevent the horse from licking/chewing at the eggs and ingesting them.


  1. Internal Parasites: Strategies for Effective Parasite Control. AAEP.
  2. Decoding Dewormers: Types, Resistence Concerns, and Use for Horses. Penn State Extension.
  3. Larval Cyathostominosis in Horses. Merck Veterinary Manual, 2019. Martin K. Nielsen, PhD, DACVM, DEVPC.
  4. Parasite Control in Horses, Merck Veterinary Manual, 2022. Allison J. Stewart, BVSc(Hons), PhD, DACVIM-LAIM, DACVECC.
  5. How To Do The Modified McMaster Fecal Egg Counting Procedure. Downloadable PDF. The University of Rhode Island and Virginia Tech. Funded by the Northeast Sustainable Agriculture Research and Education Program Project.


Article By: Kimberly S. Brown
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