OBJECTIVES: There has been increased attention to access to water, sanitation and hygiene (WASH) at schools in developing countries, but a dearth of empirical studies on the impact. We conducted a cluster-randomized trial of school-based WASH on pupil absence in Nyanza Province, Kenya, from 2007 to 2008. METHODS: Public primary schools nested in three geographical strata were randomly assigned and allocated to one of three study arms [water treatment and hygiene promotion (WT & HP), additional sanitation improvement, or control] to assess the effects on pupil absence at 2-year follow-up. RESULTS: We found no overall effect of the intervention on absence. However, among schools in two of the geographical areas not affected by post-election violence, those that received WT and HP showed a 58% reduction in the odds of absence for girls (OR 0.42, CI 0.21-0.85). In the same strata, sanitation improvement in combination with WT and HP resulted in a comparable drop in absence, although results were marginally significant (OR 0.47, 0.21-1.05). Boys were not impacted by the intervention. CONCLUSION: School WASH improvements can improve school attendance for girls, and mechanisms for gendered impacts should be explored. Incomplete intervention compliance highlights the challenges of achieving consistent results across all settings.