The aim of the present case control study was to investigate the prevalence of atypical enteropathogenic Escherichia coli (EPEC) and its possible role in causing diarrhoea among children < 5 years of age in Norway. Stool specimens received in the laboratory from children with suspected gastroenteritis (n = 251) were, in addition to routine testing, analysed for the presence of EPEC by PCR of the eae, bfpA and stx genes. Specimens from healthy children (n = 210) recruited from Maternal and Child Health Centres were analysed for EPEC only. EPEC isolates (eae+, stx-) were classified as typical (bfpA+) or atypical (bfpA-), and were tested for O : K serogroup. Information on duration of diarrhoea was recorded in a questionnaire and from referral forms. Atypical EPEC was diagnosed in 37 patients (14.7 %) compared to 21 (10.0 %) of the healthy controls [Odds ratio (OR) = 1.4, P = 0.3]. Only three isolates, all from patients, belonged to EPEC serogroups. One patient had typical EPEC. Twenty (22.5 %) of 89 patients with diarrhoea lasting > or = 14 days had atypical EPEC. The association between atypical EPEC and prolonged diarrhoea (OR = 2.1, P = 0.04) was caused by a high prevalence among female patients (40.6 %). In conclusion, atypical EPEC was found to be slightly more prevalent in patients than controls, without any overall significant association with diarrhoea. However, a significant association was observed with diarrhoea lasting 14 days or more, a finding that may indicate a role for atypical EPEC in prolonged disease.