Data from the first sentinel site (Waterloo Region, Ontario) of the Canadian Integrated Enteric Disease Surveillance System (C-EnterNet) were used in a secondary-based case-control study of laboratory-confirmed Cryptosporidium infections to study the role of various exposure factors. The incidence of cryptosporidiosis in Waterloo Region was almost double both the provincial and national rates. Persons ill with one of nine other enteric infections (amoebiasis, campylobacteriosis, cyclosporiasis, giardiasis, listeriosis, salmonellosis, shigellosis, verotoxigenic E. coli infections, yersiniosis) captured by the surveillance system were used as the control group. Of 1204 cases of enteric illness in the sentinel area between April 2005 and December 2007, 36 cases and 803 controls were selected after excluding outbreak and international travel-related cases. Univariable analyses (Pearson χ2 and Fisher's exact tests) and multivariable logistic regression were performed. Results of the multivariable analysis found that cryptosporidiosis was associated with swimming in a lake or river (OR 2·9, 95% CI 1·2–7·4), drinking municipal water (a potential surrogate for urban respondents vs. rural) (OR 2·4, 95% CI 1·04–5·7), and having a family member with a diarrhoeal illness (OR 2·9, 95% CI 1·3–6·4).