The contamination of the Walkerton, Ontario, municipal water with E. coli O157:H7 and Campylobacter in May 2000 resulted in at least 2,300 cases of gastrointestinal illness. There were 28 confirmed cases of hemolytic uremic syndrome, the most severe kidney complication. The provincial Ministry of Health and Long-Term Care determined that a study needed to be conducted on the long-term health effects associated with drinking the contaminated water. The Walkerton Health Study, a seven-year project, was established as a screening and treatment clinic to identify and treat those people experiencing illness and to study long-term health effects. This article describes the challenges, infrastructure support, staffing, and recruitment and retention efforts required to screen over 4,000 people in a yearly clinic visit. Clinical and laboratory algorithms are used to identify participants requiring specialist assessment. Design of the computer-based survey includes advanced data entry and display control, essential to ensuring accurate data for analysis. Findings from Years 1, 2 and 3 are briefly discussed.