The prevalence of infection caused by different categories of diarrhoeagenic Escherichia coli (DEC) strains, which include enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enteroinvasive (EIEC), and enterohaemorrhagic (EHEC) E. coli, in children who suffered from diarrhoea (N=3929) or did not have diarrhoea (N=1026) were analysed in two areas in Bolivia over a period of 4 years. We also analysed seasonality of DEC infections and severity of diarrhoea in children with DEC infection and compared antibiotic resistance in DEC strains isolated from children with and without diarrhoea. Stool samples were analysed for the presence of DEC by culturing followed by PCR. The most prevalent DEC categories in the samples from the children were: EAEC (11.2%); ETEC (6.6%); EPEC (5.8%); and EIEC and EHEC (<1%). DEC strains were isolated significantly more often from diarrhoea cases (22%) than from controls (17%) (p<0.001). The number of children with diarrhoea associated with EAEC, EPEC, and ETEC infections peaked in the Bolivian winter (May-September), although the proportion of DEC-positive stool samples was higher during the warm-rainy season (October-March). High levels of antibiotic resistance were detected among the DEC strains. In particular, resistance to tetracycline and sulfamethoxazole-trimethoprim was significantly higher in strains isolated from individuals with diarrhoea than in the samples from controls. The severity of disease in the children infected with EAEC, EPEC, and ETEC varied from mild to severe diarrhoea, although disease severity did not differ significantly between the different DEC categories. ETEC, EPEC, and EAEC are commonly found in Bolivia and may cause severe disease in children.