Infectious diarrhoea caused by bacterial pathogens contributes to the high level of mortality in developing countries like Bangladesh. Following standard bacteriological procedures, a total of 14 428 bacterial pathogens were isolated from 56 132 stool samples and rectal swabs collected from diarrhoeal patients between 2005 and 2008. The rate of isolation and antimicrobial susceptibility data were retrospectively analysed for these isolates and among them Vibrio spp. (42·9%) were the most predominant, followed by Shigella spp. (20·3%), Aeromonas spp. (12·8%) and Salmonella spp. (6·4%). A decreasing trend in isolation of Vibrio spp. (P<0·001) and Salmonella spp. (P<0·001) was observed. While Vibrio cholerae isolates remained susceptible to ciprofloxacin, an increase in resistance was observed in Campylobacter spp. and Shigella flexneri. Variations in susceptibility to other tested antibiotics were observed among the isolated pathogens. Access to this current data will help in understanding the local burden of diarrhoeal disease and contribute to better design of prevention programmes.