OBJECTIVE: School questionnaires of self-reported schistosomiasis provide a rapid and simple approach for identifying schools at high risk of Schistosoma haematobium and requiring mass treatment. This study investigates the reliability of school questionnaires to identify such schools and infected children within the context of a national school-based deworming programme in Kenya. METHODS: Between November 2008 and March 2009, 6182 children from 61 schools in Coast Province, Kenya were asked by an interviewer whether they had blood in urine or urinary schistosomiasis (kichocho), and their results were compared with results from microscopic examination of urine samples. Subsequently, in 2009, a school-based questionnaire survey for self-reported schistosomiasis was distributed by the Ministry of Education to all schools in Coast Province, and its results were compared against results from the parasitological survey. The questionnaire survey results were linked to a schools database and mapped. RESULTS: Prevalence of self-reported blood in urine was lower among girls than boys among all ages. The use of a 30% threshold of reported blood in urine was both highly sensitive (91.7%) and specific (100%) in identifying high (>50%) prevalence schools in Coast Province. Questionnaires were however less reliable in diagnosing S. haematobium infection in individuals, particularly among young girls. Comparable levels of reliability were observed when the questionnaire was distributed through the existing education systems and administered by class teachers. CONCLUSIONS: The results confirm that blood in urine questionnaires can be reliably used to target mass treatment with praziquantel at national scales. The mapped results of the Ministry of Education survey serve to describe the spatial variation of urinary schistosomiasis and identify schools requiring mass treatment.