Safe drinking water and hygiene are essential to reducing Kenya’s diarrhoeal disease burden. A school-based safe water and hygiene intervention in Kenya was evaluated to assess its impact on students’ knowledge and parents’ adoption of safe water and hygiene practices. We surveyed 390 students from nine schools and their parents at baseline and conducted a final evaluation of 363 students and their parents. From baseline to final evaluation, improvement was seen in students’ knowledge of correct water treatment procedure (21-65%, P<0.01) and knowing when to wash their hands. At final evaluation, 14% of parents reported currently treating their water, compared with 6% at baseline (P<0.01). From 2004 to 2005, school absenteeism in the September-November term decreased in nine project schools by 35% and increased in nine neighbouring comparison schools by 5%. This novel programme shows promise for reducing school absenteeism and promoting water and hygiene interventions in the home.