We determined prospectively the incidence of childhood diarrhoea associated haemolytic uraemic syndrome (D+ HUS) or HUS due to Streptococcus pneumoniae (SP+ HUS) in Canada through the Canadian Paediatric Surveillance Program (CPSP) network. From April 2000, to March 2002, 82% (1,886/2,300) of all Canadian paediatricians reported possible new cases of D+ HUS or SP+ HUS. Diagnosis was validated with a second questionnaire. There were a total of 136 children with D+ HUS (epidemic, n =15; endemic, n =121), corresponding to an annual incidence rate of 1.11 cases per 100,000 children under 16 years of age. Excluding incomplete forms, the annual incidence rate among endemic cases was 0.74 cases per 100,000. The provinces of Ontario (40%), Quebec (31%), and Alberta (18%) accounted for 89% of cases. Evidence of E. coli O157 or O157:H7 were found in 94% (79/84) of children who had positive stool cultures. The mortality rate was 4% (n =5) and 34% (n =41) of children underwent dialysis for a median of 12 days (2-60 days). SP-HUS was diagnosed in four children with pneumonia and pleural effusion (n =2) or meningitis (n =2) who survived. One child with positive direct Coombs testing had definitive evidence of SP+ HUS. The remaining three were considered possible cases. We conclude that SP+ HUS is rare in Canada. Over the last 15 years, the incidence of childhood D+ HUS in Canadian children may have decreased.