The purpose of the study was to investigate the association of CLTS to the reduced household morbidity in Nyando District. Descriptive statistics was used to assess the diarrhoea prevalence, knowledge, uptake and practices on CLTS; Chi-square test was used to compare proportions between control and intervention sites. Association between CLTS and diarrhoea occurrence was done using binary logistic regression where diarrhoea occurrence was the outcome and CLTS or non CLTS sites were the independent variables. The study adopted a comparative cross sectional study design comparing the disease prevalence of households within intervention sub location of Kochogo Central where CLTS was implemented and the disease prevalence of households within non intervention sub location of Wang’ang’a where CLTS has not been implemented. A total of 305 household heads or proxies (102 interventions and 203 non interventions) were interviewed and data on number of cases of diarrhoea, cholera and bilharzia that any member of the household had experienced in the prior 6 months before the survey was collected.