Aims: To measure enteric bacterial contamination of tubewells in three flood prone areas in Bangladesh and the relationship of bacteriological contamination with tubewell sanitary inspection scores. Methods and Results: Microbiologists selected 207 tubewells in three flood prone districts, assessed physical characteristics of the tubewells and collected a single water sample from each tubewell. Tubewell water samples were contaminated with total coliforms (41%, n = 85), thermotolerant coliforms (29%, n = 60) and Escherichia coli (13%, n = 27). Among contaminated wells, the median CFU of contamination per 100 ml was 8 (interquartile range, 2-30) total coliforms, 5 (interquartile range, 2-23) thermotolerant coliforms and 6 (interquartile range, 1-30) E. coli. There was no significant association between tubewell contamination with E. coli, thermotolerant coliforms or total coliforms and a poor sanitary inspection score, though a history of inundation was associated with contamination with both E. coli and thermotolerant coliforms. Conclusions: Tubewells in flood-prone regions of Bangladesh were commonly contaminated with low levels of faecal organisms, contamination that could not be predicted by examining the tubewell's external characteristics. Significance and Impact of the Study: The forms currently used for sanitary inspection do not identify the most important causes of drinking water contamination in these communities.