During the spring of 1993 an estimated 403000 residents of the greater Milwaukee, Wisconsin area experienced gastrointestinal illness due to infection with the parasite Cryptosporidium parvum following contamination of the city's water supply. To define the clinical, laboratory and epidemiologic features of outbreak-associated cryptosporidiosis in children, medical and laboratory records for all children submitting stool samples to the microbiology laboratory of the Children's Hospital of Wisconsin between 7 April and 13 May 1993 were reviewed retrospectively. Interviews with parents were also conducted to obtain additional clinical history. Cryptosporidium, as the sole pathogen, was identified in stools from 49 (23%) of the 209 children enrolled in the study. Children with laboratory-confirmed cryptosporidiosis were more likely to live in areas of Milwaukee supplied with contaminated water (RR=1·92, CI=1·19–3·09), to be tested later in their illness (P<0·05), to have submitted more than one stool specimen (P=0·01), to have an underlying disease that altered their immune status (RR=2·78, CI=1·60–4·84), and to be older than 1 year of age (RR=2·02, CI=1·13–3·60). Clinical illness in these patients was more prolonged and associated with weight loss and abdominal cramps compared with Cryptosporidium-negative children. In the context of this massive waterborne outbreak relatively few children had documented infection with Cryptosporidium. If many children who tested negative for the parasite were truly infected, as the epidemiologic data suggest, existing laboratory tests for Cryptosporidium were insensitive, particularly early in the course of illness.