Dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science Johannesburg, 2012 / Introduction: Diarrhoea is a major cause of mortality and morbidity amongst children under five years of age worldwide. Aim: To characterise the bacterial aetiologies and molecular characterises the pathogens associated with hospitalization for diarrhoeal disease among South African children aged less than 5 years Methods: Children aged < 5 years hospitalized with diarrhoea were enrolled. Standard microbiological methods (culture, biochemical tests, serotyping) and molecular methods (PCR) were used, targeting bacterial pathogens such as diarrhoeagenic Escherichia coli (DEC), Salmonella species, Shigella species, Vibrio cholerae and Campylobacter species. Results: A total of 1816 stool specimens were processed, of which 633 (35%) were positive for enteric bacterial pathogens. Isolates in order of frequency included 562 DEC, 49 Shigella spp., 20 Salmonella spp., 2 Campylobacter spp. There were 48 (8%) enteric bacterial infections identified with more than one pathogen. Co-infections of bacterial pathogens with other organisms include 52 bacterial agents concurrent with Cryptosporidium co-infection, 128 with rotavirus coinfection and 9 episodes which included Cryptosporidium and rotavirus co-infections. Conclusion: The overall recovered bacterial pathogens from stool specimens was 35% with DEC being the most commonly identified.