Acute gastroenteritis (AGE) is one of the most common diseases among children and an important cause of school absenteeism. The aim of this study was to assess the effectiveness of a handwashing program using hand sanitizers for the prevention of school absenteeism due to AGE. A randomized, controlled and open study of a sample of 1341 children between 4 and 12 years of age, attending 5 state schools in Almería (Spain), with an 8-month follow up (academic year). The experimental group (EG) washed their hands with soap and water, complementing this with the use of a hand sanitizer, and the control group (CG) followed the usual handwashing procedure. Absenteeism rates due GI were compared between the 2 groups through the multivariate Poisson regression analysis. Percent days absent in both groups were compared with a Z-test. 446 cases of school absenteeism due to AGE were registered. The school children from the EG had a 36% lower risk of absenteeism due to AGE (IRR: 0.64, 95% confidence interval: 0.52-0.78) and a decrease in absenteeism of 0.13 episodes/child/academic year (0.27 of EG vs 0.40 CG/episodes/child/academic year, P < 0.001). Pupils missed 725 school days due to AGE and absent days was significantly lower in the EG (EG: 0.31%, 95% confidence interval: 0.28-0.35 vs. CG: 0.44%, 95% confidence interval: 0.40-0.48, P < 0.001). The use of hand sanitizer as a complement to handwashing with soap is an efficient measure to reduce absent days and the number of school absenteeism cases due to AGE.