The aim of this study was to assess the effect of fluoride on the severity of caries among children exposed to different concentrations of fluoride in the drinking water and living in rural areas in the Sudan. Permanently resident schoolchildren (n = 299) aged 11-13 years from three villages were clinically examined under field conditions. The caries criterion was teeth in need of extraction or extracted; only molars were recorded. Dental fluorosis was scored on all buccal tooth surfaces by the Thylstrup and Fejerskov index. The fluoride concentrations of the drinking water were assessed in samples (n = 25) collected from wells and households. Predictors of caries were assessed by logistic regression analyses. There was no significant difference regarding age and gender distribution between the areas (P > 0.05, df = 2, Kruskal-Wallis test). The socio-economic conditions in these villages were presumed to be equal. Significantly different fluoride concentrations in the drinking water were verified by the severity of dental fluorosis. Children in Abu Delaig, drinking water with 1.0-2.0 mg fluoride/L (median = 1.8), had significantly higher caries prevalence (21% versus 8%) than in a 0.4 mg fluoride area. Area was the only significant predictor for caries; odds ratio 3.7 for children in Abu Delaig compared with the low fluoride area. There was no difference in caries prevalence between the lowest and the highest fluoride (2.9 mg) area. This study failed to demonstrate an effect of fluoride in drinking water on caries experience when the end point was molars indicated for extraction or missing because of caries.