The incidence and causes of infectious intestinal disease (IID) in children aged <5 years presenting to general practitioners (GPs) were estimated. During a 12-month period, soiled nappies were collected from children presenting with symptoms suggestive of IID in a network of 65 GPs located across England. Molecular methods were used to detect a range of enteric pathogens including viruses, bacteria and parasites. Genotyping was performed on rotavirus and norovirus isolates. A total of 583 nappies were collected from 554 children; a pathogen was detected in 361 (62%) specimens. In the 43 practices 1584 new episodes of IID were recorded in a population averaging 19774; the specimen capture rate was 28%. IID incidence peaked during March and April. Norovirus (24·5%), rotavirus (19·0%) and sapovirus (12·7%) were most commonly detected, and mixed infections were detected in 11·7% of cases. Strain characterization revealed G1P (65·8%), G4P (8·1%) and G9P (8·1%) as the most common rotavirus genotypes, similar to the UK national distribution. GII-3 (42·9%) and GII-4 (39·7%) were the most common norovirus genotypes; this was significantly different (P<0·005) to the national distribution.