Introduction: Intestinal Escherichia coli pathogens are major causes of diarrhoeal disease in children under five years of age worldwide. The aim of this study is to evaluate the association of E. coli pathotypes with childhood diarrhoea in Colombia. Methodology: A case-control study was conducted in 815 samples from children younger than five years of age in Cartagena, Colombia (466 cases and 349 controls). Controls were randomly selected 1:1 to cases, to obtain 349 cases and 349 controls. Results: This study revealed that 27 (7.44%) cases and 12 (3.43%) controls were positives for any of the E. coli pathotypes. The difference observed was statistically significant indicating that E. coli pathotypes were associated with cases of childhood diarrhoea. Enterotoxigenic E. coli (ETEC) was the most common pathotype associated with childhood diarrhoea. Additional E. coli pathotypes were also identified. Conclusions: We conclude that after the adjustment by age, sex and socioeconomic stratum, the odds ratio obtained by logistic regression shows an association between infection with ETEC and childhood diarrhoea.