Despite continued national and international efforts, access to improved water and sanitation remains limited in many developing countries. The health consequences of lacking access to clean water and proper sanitation are severe, and particularly among children. Sixty-two percent and thirty one percent of all deaths in Africa and Southeast Asia, respectively, are caused by infectious disease associated with WASH. Poor access to safe drinking water, inadequate sanitary conditions and poor hygiene practices play major roles in the increased burden of communicable disease in developing countries and especially diarrhoeal skin/eye infections, intestinal worms and respiratory infections. It is estimated that 88% of diarrhoeal diseases are attributed to unsafe water supply, inadequate sanitation and hygiene. The main objective of this study was to asses the determinants of water, sanitation and hygiene related morbidity amongst school children in Mathare informal settlement in Nairobi, Kenya. The study adopted a descriptive research design, involving 342 randomly selected pupils from 20 primary schools. Semi structured questionnaires and interviews were used. The results showed that water unavailability in school (Exp B=47.9, p value-0.008); lack of hand washing facilities in school (Exp B 22.5, p value-0.04); Pupil toilet ratio above 1:25 (Exp B 3715.8, p value-0.000 ), School has no health clubs (Exp B 11.9, p value-0.08 ); Pupils do not wash hands with soap (Exp B 810.9, p value-0.003 ), Pupils don‘t wash face (Exp B (0.002, p value-0.000 ); pupils don‘t bathe with soap (Exp B 47.2, p value-0.017); High knowledge level (Exp B 0.012, p value-0.006); Low knowledge level (Exp B 1.94, p value-0.007) significantly influenced WASH related morbidity among pupils. It is concluded that WASH knowledge, Hygiene practices and supportive institutional factors in primary schools in Mathare, are significant determinants linked to WASH morbidity in school going children. The study recommends that a holistic and multifaceted approach be used by the Government, NGOs and School management to address WASH morbidity in schools. WASH education directed at strengthening knowledge that the schools already have should be reinforced; promotion of hygiene practices and supportive infrastructure/ social support should all be addressed together so as to successfully and directly reduce diarrhoeal diseases, skin/eye infections and promote health among the children.