OBJECTIVES: Waste incineration releases a mixture of chemicals with high embryotoxic potential, including heavy metals and dioxins/furans, into the atmosphere. In a previous ecological study we found an association between the risk of urinary tract birth defects and residence in the vicinity of municipal solid waste incinerators (MSWIs). The objective of the present study was to specifically test this association. METHODS: A population-based case-control study compared 304 infants with urinary tract birth defects diagnosed in the Rhône-Alpes region (2001-2003) with a random sample of 226 population controls frequency-matched for infant sex and year and district of birth. Exposure to dioxins in early pregnancy at the place of residence, used as a tracer of the mixture released by 21 active waste incinerators, was predicted with second-generation Gaussian modelling (ADMS3 software). Other industrial emissions of dioxins, population density and neighbourhood deprivation were also assessed. Individual risk factors including consumption of local food were obtained by interviews with 62% of the case and all control families. RESULTS: Risk was increased for mothers exposed to dioxins above the median at the beginning of pregnancy (OR 2.95, 95% CI 1.47 to 5.92 for dioxin deposits). When only interviewed cases were considered, risk estimates decreased mainly because the non-interviewed cases were more likely to live in exposed residential environments (OR 2.05, 95% CI 0.92 to 4.57). The results suggest that consumption of local food modifies this risk. CONCLUSIONS: This study confirms our previous observation of a link between the risk of urinary tract birth defects and exposure to MSWI emissions in early pregnancy and illustrates the effect of participation bias on risk estimates of environmental health impacts.