Background Management of patients with human immunodeficiency virus (HIV) infection using highly active antiretroviral therapies (HAART) has improved health outcomes, including reduced opportunist infections like diarrhoea. However, there are reports of Escherichia coli strains as notable agent of opportunistic infections (OI) in HIV-positive patients. It is important to know the pathotypes that are involved to efficiently and effectively manage the patients. Methods This study examined the pathotypes of Escherichia coli in the stools of volunteer HIV-positive adult individuals attending HAART Clinic in IleIfe, Nigeria that presented with diarrhoea. E. coli was isolated from the stool samples, characterised, identified, and pathotyped based on the presence of virulence genes: eaeA, bfpA, stx1, stx2, eltB, estA, ipaH, pCVD, and EcoRI-PstI. Results E. coli was found in only 27 (9.96%) of the 271 stool samples examined. Among the 72 E. coli strains isolated, 21 were Diarrheagenic (DEC): 11 (52.38%) were Enteropathogenic E. coli (EPEC), 7 (33.33%) were Shiga toxin-producing E. coli (STEC), and 3 (14.29%) were E. coli (EHEC) pathotypes. Five (5) of the stool samples yielded more than one DEC pathotype. Conclusion There was a low prevalence of DEC, and Enteropathogenic E. coli (EPEC), Shiga toxin-producing E. coli (STEC), and Enterohaemorrhagic E. coli (EHEC) are major pathotypes of diarrheagenic Escherichia coli prevalent among the HIV-positive adult individuals in the study area.