School-based hygiene and water treatment programs increase student knowledge, improve hygiene, and decrease absenteeism, however health impact studies of these programs are lacking. We collected baseline information from students in 42 schools in Kenya. We then instituted a curriculum on safe water and hand hygiene and installed water stations in half ("intervention schools"). One year later, we implemented the intervention in remaining schools. Through biweekly student household visits and two annual surveys, we compared the effect of the intervention on hygiene practices and reported student illness. We saw improvement in proper handwashing techniques after the school program was introduced. We observed a decrease in the median percentage of students with acute respiratory illness among those exposed to the program; no decrease in acute diarrhea was seen. Students in this school program exhibited sustained improvement in hygiene knowledge and a decreased risk of respiratory infections after the intervention.