Socio-behavioural factors and pathogens associated with childhood diarrhoea are of global public health concern. Our survey in 696 children aged ⩽2 years in rural West Bengal detected rotavirus as sole pathogen in 8% (17/199) of diarrhoeic stool specimens. Other organisms were detected along with rotavirus in 11% of faecal specimens. A third of the children with rotavirus diarrhoea, according to Vesikari score, had severe illness. The top four rotavirus genotypes were G9P (28%), G1P (19%), G2P (14%) and G8P (8%). In the multivariate model, the practice of ‘drawing drinking water by dipping a pot in the storage vessel’ [adjusted odds ratio (aOR) 2·21, 95% confidence interval (CI) 1·03–4·74, P = 0·041], and ‘children aged ⩽6 months with non-exclusive breastfeeding’ (aOR 2·07, 95% CI 1·1–3·82, P = 0·024) had twice the odds of having diarrhoea. Incidence of rotavirus diarrhoea was 24/100 child-years in children aged >6–18 months, 19/100 child-years in children aged >18–24 months and 5/100 child-years in those aged ⩽6 months. Results have translational implications for future interventions including vaccine development.