Worldwide, lack of access to safe drinking water together with inadequate sanitation and hygiene is an overwhelming contributor to approximately 4 billion cases of illness annually. This study was set out to understand the effects of hygiene and sanitation interventions on targeted health outcomes including diarrhoeal prevalence in children’s of Turkana District, Kenya. The interventions undertaken included capacity building and empowerment approach to trigger communities to demand hygiene and sanitation facilities. Three hundred mothers were randomly sampled in a baseline survey carried out in 2007 and in a post-intervention survey carried out in 2008 (a repeat cross-sectional study design). Specimens were collected for microbiological tests of key diarrhoea related pathogens. Overall, Faecal coliform counts per 100 ml sample had significant variations between 2007 and 2008; in Kakuma, reduced from 88 to 30.2 colony units (P = 0.005), Lodwar Central where the number reduced from 91 to 17.3 units (P = 0.003), and in Lokichogio Division, the number reduced from 63.8 to 23.6 units (P = 0.006). From the 230 stool samples examined, the proportion of children from whom infectious pathogens of Proteus spp. was isolated reduced from 16 to 7 % while Escherichia coli reduced from 54 to 41 %. Overall, prevalence of diarrhoea related microbes in children aged <5 years reduced from 91.3 % in 2007 to 78.3 % after intervention (2008). It is notable that sanitation and hygiene promotion leads to significant reduction of diarrhoea prevalence in children aged <5 years. Its application should therefore be up-scaled in resource constrained areas.