Abstract. We conducted a matched-control trial in Mali to assess the effectiveness of a comprehensive school-based water, sanitation, and hygiene (WASH) intervention on pupil absence, diarrhea, and respiratory infections. After completion of the intervention, data were collected from 100 beneficiary schools and 100 matched comparison schools in 5-6 sessions over a 14-month period. Data collection included roll calls to assess absenteeism and interviews with a subset of pupils to assess recent absence and disease symptoms. The odds of pupils being absent at roll call were 23% higher in beneficiary schools than in comparison schools (odds ratio [OR]: 1.23, 95% confidence interval [CI]: 1.06, 1.42). The odds of pupils reporting being absent due to diarrhea (OR: 0.73, 95% CI: 0.56, 0.94) or having had diarrhea (OR: 0.71, 95% CI: 0.60, 0.85) or respiratory infection symptoms (OR: 0.75, 95% CI: 0.65, 0.86) in the past week were lower in beneficiary schools compared with comparison schools. We found that a school-based WASH intervention can have a positive effect on reducing rates of illness, as well as absence due to diarrhea. However, we did not find evidence that these health impacts led to a reduction in overall absence. Higher absence rates are less likely attributable to the intervention than the result of an imbalance in unobserved confounders between study groups.