Nosocomial diarrhoea, defined as diarrhoea occurring more than 72 h after hospital admission, is reported to account for <1% of endemic nosocomial infections and 17% of epidemic nosocomial infections. The yield of diagnoses from stool cultures in nosocomial diarrhoea is low, and information regarding the role of parasites is limited. We conducted a study to determine the responsible bacterial and parasitological pathogens from nosocomial diarrhoea cases in our 2000-bed tertiary care facility over a 16-month period. Of 226 patients, Clostridium difficile toxins A or B were present in 5.5%, giardia cysts and/or trophozoites in 4.4%, Blastocytis hominis in 4.4% and Cryptosporidium sp. in 0.5% of samples. In conclusion, parasites should be sought in nosocomial diarrhoea in endemic areas.