The study identified the common aetiological agents and prominent clinical features of dysentery cases in children aged <5 years and compared this to non-dysentery diarrhoeal cases from the same population. From January 2010 to December 2011, 2324 children aged <5 years received treatment at Kumudini Hospital, of which 682 (29%) presented with dysentery. Of the dysenteric children, aetiology could not be determined for over half (61%). Shigella spp. accounted for 32% of dysentery cases. Significant associations were found between presence of blood in stool and: child age (24–59 months) [odds ratio (OR) 2·21, 95% confidence interval (CI) 1·49–3·27], no treatment of drinking water at home (OR 2·00, 95% CI 1·09–3·67), vomiting (OR 0·19, 95% CI 0·14–0·25), abdominal pain (OR 4·68, 95% CI 3·24–6·77), straining (OR 16·45, 95% CI 11·92–22·69), wasting (OR 1·66, 95% CI 1·15–2·41), and presence of Shigella in stool (OR 6·25, 95% CI 4·20–9·29) after controlling for confounders. This study makes it clear that appropriate public health strategies are needed to reduce the burden of dysentery in Bangladesh.