BACKGROUND: There is an increasing importance of pet-transmitted infections, some of those are considered emerging infections. AIM: To determine the species and frequency of intestinal parasites in pets with diarrhea (hemorrhagic gastroenteritis excluded). MATERIAL AND METHODS: A descriptive retrospective study. Fecal samples from 972 dogs and 230 cats consulting in two veterinary practices in Santiago, between 1996 and 2003, were studied using Burrows' technique. RESULTS: Protozoa were found in 64.8% of dogs and in 66.5% of cats; helminthes in 24% of dogs and 45.2% of cats. The species found in dogs were Blastocystis sp. in 36%, Ameba sp. in 31%, Giardia intestinalis in 22%, Toxocara canis in 11%, Chilomastix sp. in 10%, Isospora sp. in 9%, Trichuris vulpis in 9%, Trichomonas sp. in 5%, Sarcocystis sp. in 4%, Dipylidium caninum in 2%, Ancylostomideos in 2%, Toxascaris leonina in 1%, Physaloptera sp. in 1%, Taenia sp. in 0.4%. Species found in cats were Blastocystis sp. in 37%, Ameba sp. in 30%, G intestinalis in 19%, Chilomastix sp. in 12%, Isospora sp. in 12%, Toxocara cati in 10%, D caninum in 7%, Sarcocystis sp. in 5%, Trichomona sp. in 5%, Toxoplasma gondii in 4%, Taenia sp. in 2% and Physaloptera sp. in 1%. Forty eight percent of parasites found in dogs and 49% found in cats have zoonotic potential. In dogs younger than six months Blastocystis sp., Ameba sp., G intestinalis, Chilomastix sp., Isospora sp. and T canis were significantly more common; the same was observed for Isospora in young cats. Approximately 60% of infected animals bore more than one parasite. CONCLUSIONS: A high rate of intestinal parasitism in pets with diarrhea was found; an important proportion of them have zoonotic potential.