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Background  The distribution of and factors associated with intestinal parasitic infections are poorly defined in high risk vulnerable populations such as urban slums in tropical sub-Saharan Africa.    Methods  In a cross sectional study, children aged 5 years and below who presented with diarrhoea were recruited from selected outpatient clinics in Mukuru informal settlement, and from Mbagathi District hospital, Nairobi, over a period of two years (2010–2011). Stool samples were examined for the presence of parasites using direct, formal-ether concentration method and the Modified Ziehl Neelsen staining technique.    Results  Overall, 541/2112 (25.6%) were positive for at least one intestinal parasite, with the common parasites being;  Entamoeba histolytica,  225 (36.7%), Cryptosporidium spp . 187, (30.5%),  Giardia lamblia , 98 (16%).The prevalence of intestinal parasites infection was higher among children from outpatient clinics 432/1577(27.4%) than among those admitted in hospital 109/535 (20.1%) p < 0.001. Infections with  E. histolytica , and  G. lamblia  were higher among outpatients than inpatients (13.8%  vs  1.3% p < 0.001 and 5.8%  vs  1.3% p < 0.049) respectively, while infection with  Cryptosporidium spp . was higher among inpatients than outpatients (15.3%  vs  6.7%) respectively p < 0.001. Other parasites isolated among outpatients included  Isospora belli , 19 (1.2%),  Ascaris lumbricoides,  26 (1.6%), and  Hymenolepis nana  12 (0.8%), with the remainder detected in less than ten samples each. HIV-infected participants were more likely to be infected with any parasite than uninfected participants, Adjusted Odds Ratio (AOR), 2.04, 95% CI, 1.55-2.67, p < 0.001), and with  Cryptosporidium spp . (AOR, 2.96, 95% CI 2.07-4.21, p < 0.001).The inpatients were less likely to be infected with  E. histolytica  than outpatients (AOR, 0.11, 95% CI, 0.51- 0.24, p < 0.001), but more likely for inpatients to be infected with  Cryptosporidium spp . than outpatients (AOR, 1.91, 95% CI, 1.33-2.73, p < 0.001). Mixed parasitic infections were seen in 65 (12.0%) of the 541 infected stool samples.    Conclusion  Intestinal parasitic infections are common in urban informal settlements’ environment. Routine examinations of stool samples and treatment could benefit both the HIV infected and uninfected children in outpatient and inpatient settings.

Intestinal parasitic infections in children presenting with diarrhoea in outpatient and inpatient settings in an informal settlement of Nairobi, Kenya