Introduction: bacterial agents are among pathogens implicated to cause diarrhea in children resulting to huge mortality and morbidities. Bacterial etiologies causing diarrhea in children below five years are rarely investigated in Central Kenya, which would otherwise guide prescription and target health education.

Methods: a cross-sectional study approach was applied on 163 randomly selected stool samples from children below five years who presented with diarrhea in Murang`a and Muriranja`s hospitals. The objective was to determine the bacterial agents of diarrhea. Enteric bacterial pathogens were cultured using appropriate media and identified. Statistical analyses were performed using STATA v.13. Chi-square or Fisher exact-test were used to check for evidence of relationship whenever applicable.

Results: there were nearly equal distributions in gender 86 (52.8%) female vs. 77 (47.2%) male, majority (35.6%) aged between 0-12 months. Bacterial isolates were highly diverse in female than the male, children aged 49-60 months and least among those aged 0-12 months. A total of 188 bacterial isolates belonging to 11 genera were recovered. The predominant bacteria was nonpathogenic Escherichia coli 85 (45.2%), while 13 (6.9%) Escherichia coli were positive for virulence genes, including 8 (4.3%) positive for LT and STp Shiga-like or Enterotoxigenic Escherichia coli, 3 (1.6%) positive for eae and bfpA Enteropathogenic Escherichia coli and 2 (1.1%) positive for Enteroaggregative Escherichia coli gene. Others included: Salmonella 21 (11.2%), Pseudomonas 14 (7.4%), Shigella 14 (7.4%), Klebsiella 12 (6.4%), Aeromonas 8 (4.3%), Enterobacter 7 (3.7%), Proteus 8 (4.3%), Citrobactor 3 (1.6%), Yersinia 2 (1.1%) and Vibrio 1 (0.5%).

Conclusion: salmonella was the major bacterial isolate and majority of the bacteria were statistically significant cause of diarrhea (p=0.001).