This study reports the prevalence of Cryptosporidium, Giardia and Isospora species in cats showing signs of gastrointestinal disease. Records from a United Kingdom commercial diagnostic laboratory between December 2003 and December 2005 were reviewed. Of 1355 cats, Cryptosporidium species oocysts were found in 13 cats (1%), Giardia species trophozoites in 74 (6%), and Isospora felis oocysts in 46 (3%). In a second group of 48 cats, prevalence of Giardia species was 15% using an immunoassay for detection of antigen compared to 4% detected with microscopy. Prevalence of Giardia (9%) and Isospora (9%) species was higher in cats less than 6 months old. Gender and breed did not affect prevalence. There was a trend for Cryptosporidium and Isospora species infections to be detected in late autumn and early winter. Regional differences in prevalence were not detected. None of these organisms show a characteristic pattern of clinical signs. This study demonstrates that enteric protozoal infection is common in domestic cats showing signs of alimentary disease.