To determine the effect of a school-based weekly iron supplementation delivery system (WISDS) on the prevalence of anemia among anemic schoolchildren. Two hundred and forty-two Filipino schoolchildren aged 6-12 years with hemoglobin (Hb) concentration <12 g/dl and enrolled for school year 2003-2004. UNICEF iron-folate tablets containing 60 mg elemental iron and 0.40 mg folic acid were given weekly through directly observed supplementation by the teachers for 27 weeks. Compliance to iron supplementation was monitored by the teachers and was recorded using a monitoring form and a supplementation calendar. Hb concentration, weight and height were determined at baseline and at post-intervention. At post-intervention, the participants' mean Hb concentration increased by 0.4 g/dl (95% confidence interval =0.3, 0.5 g/dl; P<0.0001), anemia prevalence was reduced by 53.7, and 84.3% of the participants had 100% compliance to supplementation. The school-based WISDS reduced anemia prevalence among anemic schoolchildren and resulted in high compliance to and coverage of iron supplementation.