Notwithstanding significant advancement in the understanding of pathogenesis and management, diarrheal illnesses remain one of the principal causes of global childhood mortality and morbidity. Infections account for most illnesses, with pathogens employing ingenious mechanisms to establish disease. In 2002, an interdisciplinary program “Populations et al. Espaces à Risques SANitaires” (PERSAN) was set up under the patronage of the Development Research Institute (IRD). Focused on health in Cameroon’s urban environment, the program mainly sought to identify diarrhea risk factors in Yaoundé. So for, a cross-sectional epidemiological study in children aged 6–59 months was carried out using a standardized protocol. The survey was initiated in 2002 and conducted during April to June in the year 2005. 3,034 stool samples were collected from children in twenty neighbourhoods in Yaoundé and examined at the Epidemiology and Public Health Laboratory of the Cameroon Pasteur Institute. About 60% of the patients were aged less than two years and 52% were male. Among the 437 patients with the diarrheal disease, 260 were found to be of infectious etiology, i.e. micro organism was detected in 59.5 % of the cases. Out of which, 10 (03.8%), 96 (36.9%), and 154 (59.2%) were respectively caused by pathogenic viruses, pathogenic bacteria and pathogenic parasites. Higher prevalence was found in overcrowded and under supply spontaneous settlement (78.4%) than in less crowded and formal residential settlement (21.5%). Etiologic data on diarrheal diseases and their spatial distribution are important tools for public health management and control strategic planning.