The main intestinal parasites in horses are bots, large strongyles, small strongyles, pin worms, and tapeworms.  Although there are over 100 species of parasites that affect horses, Dr. Eugene Lyons indicates about 50% of them belong to the small strongyle group.  Large strongyles have historically been the most damaging to the horse but the dewormers of today are very effective against these parasites and if horses are dewormed correctly, they usually do not cause a lot of problems.  Small strongyles have become the major problem for horses because the larval stages migrate into the large intestine where they encyst and are not killed by regular dewormers.  Also, many of the small strongyles have become resistant to common dewormers and no new classes of dewormer compounds have been developed in the last 20 years.  Resistance has been found in all of the routine equine dewormers except for ivermectin and moxidectin and it is possible resistance will develop in the future to these products as well. 

It is now recommended by some to only deworm horses with high numbers of worm eggs in their feces.  Using less dewormer decreases the chance of resistance.  This sounds good on paper but to be effective fecal exams must be checked often to make sure significant parasite infections are not occurring.  The other concern about using egg counts to determine when to deworm is that the larval encysted small strongyles that were mentioned earlier do not produce eggs so you could have a large number of small strongyle larvae but a negative fecal egg count.  It is important to follow advice from your vet to develop an effective deworming program