Pathogenic Escherichia coli are of different types, currently grouped into six groups depending on the virulence gene(s) they possess. This study isolated pathogenic E. coli from 580 stool samples obtained in the month of August, 2016. The samples were obtained from asymptomatic school going children in one of the biggest urban slums in Kenya. Ten primary schools were randomly sampled and 40 to 80 stool samples collected from each school depending on the school population. Both gender and age were considered when sampling. Data obtained was analysed using single factor ANOVA to test association between school location and levels of infection with pathogenic bacteria. A total of 244 (17%) samples had E. coli. Out of these, 38 (6.5%) were shown to have one or a combination of the pathogenic genes, namely: ipaH, virF, st2, daaE, eae, aafII, stx1, bfp, lt and stII and were thus classified into seven groups. Of the pathogenic isolates 35 (21.2%) were multidrug resistant. There was an association between school location and the prevalence of pathogenic bacteria. In conclusion, asymptomatic school going children in the slum were found to be infected with multidrug resistant pathogenic E. coli.