The prevalence of various pathotypes of Escherichia coli was investigated during a case-control study conducted in children diarrhoea in Yaoundé. Isolates obtained from the stools samples of children aged 6 months to 5 years were selected on phenotypic basis, and identified by virulence genes detection using polymerase chain reactions. The most prevalent pathotype was enteroaggregative Escherichia coli (25.8%). Enteropathogenic Escherichia coli (3.6%), enterotoxigenic Escherichia coli (1%), and enteroinvasive Escherichia coli (0.2%) followed. No shiga toxin-producing Escherichia coli were identified. Enteroaggregative Escherichia coli was not associated with diarrhoea (cases 26.1%, controls 25.5%; P=0,887), unlike enteropathogenic Escherichia coli (cases 6.7%, controls 1%; P=0.003). Investigations into documented potentials of enteroaggregative Escherichia coli in causing diarrhoea and other related pathologies indicated that it could be a major public health threat in Cameroon despite the fact that it was not found associated with clinical diarrhoeal cases in this study.