Giardia intestinalis and Cryptosporidium spp. are commonly identified intestinal pathogens in humans and animals. In light of the clinical disease, production losses and zoonotic potential of both Giardia and Cryptosporidium infections, a study was undertaken to investigate the prevalence of these parasites in cattle, sheep, pigs and horses in Canadian farms at different geographical locations. A total of 104 cattle, 89 sheep, 236 pigs and 35 horses were sampled from 15 different Canadian geographical locations. Fecal samples were examined after concentration and immunofluorescent staining. Giardia and Cryptosporidium were present in cattle and sheep in six out of six sites sampled. In cattle the overall prevalence was 29% for Giardia and 20% for Cryptosporidium. Giardia was identified in 38% of sheep while 23% of sheep were positive for Cryptosporidium. Giardia and Cryptosporidium were identified in four out of six hog operations with an overall prevalence of 9% for Giardia and 11% for Cryptosporidium. All horse sampling locations (4/4) were positive for Giardia with 20% of animals infected. Cryptosporidium was identified in three out of four sampling sites with a prevalence of 17%. The prevalence of Giardia and Cryptosporidium was greater in calves and lambs compared to adults. This study demonstrates that both Giardia and Cryptosporidium appear to be prevalent in farm livestock.