HIV infection is an established risk for diarrhoeal severity, less is known about specific enteric pathogens associated with HIV status. We determined associations of selected enteric pathogens with HIV infection and HIV exposure among Kenyan children.A cross-sectional study among 6 months to 15 year olds presenting to two Western Kenya District hospitals with acute diarrhoea between 2011 and 2013.Stool was tested using standard bacterial culture and microscopy for ova and parasites. HIV status was obtained from children and mothers. Enteric pathogen prevalence was compared between HIV-infected and HIV-uninfected children and between HIV-exposed uninfected (HEU) and HIV-unexposed. Unadjusted and adjusted prevalence ratios for selected pathogens by HIV status were estimated using relative risk (RR) regression. Age, site, income, household crowding, water source/treatment, anthropometrics, cotrimoxazole use and breastfeeding history were accounted for in multivariable models.Among 1076 children, median age was 22 months (interquartile range: 11-42 months), 56 (5.2%) were HIV-infected and 105 (11.3%) of 926 HIV-uninfected children in whom maternal HIV status was obtained were HIV-exposed. The following organisms were most frequently isolated from stool: enteroaggregative Escherichia coli (13.3%), Giardia species (spp.) (11.1%), Campylobacter spp. (6.3%), enteropathogenic E. coli (EPEC) (6.1%) and Cryptosporidium spp. (3.7%). Accounting for age, HIV-infection was associated with typical EPEC infection (prevalence ratio 3.70, P = 0.002) while HIV-exposure was associated with Cryptosporidium among HIV-uninfected children (prevalence ratio 2.81, P = 0.005).EPEC and Cryptosporidium infections were more common in HIV-infected and HIV-exposed children, respectively. This could explain the increased mortality attributed to these pathogens in other studies. Interventions targeting EPEC and Cryptosporidium may reduce morbidity and mortality in high HIV-prevalence settings.