School-based deworming programmes have been promoted as a cost-effective strategy for control of nematode infection in developing countries. While numerous efficacy studies have been conducted, there is little information on actual programme effectiveness in areas of intense transmission. A randomized trial of a school-based deworming programme was conducted in 12 primary schools on Pemba Island, Zanzibar. Four schools each were randomized to control, twice a year deworming with single dose mebendazole or three times a year deworming. Baseline and 12-month follow-up data on helminth infection using the Kato-Katz technique, demographic information and nutritional status were collected on 3028 children from March 1994 to May 1995. Intensity of infection measured as eggs per gram of faeces (epg) declined significantly for Ascaris lumbricoides, Trichuris trichiura and hookworm infections in both treatment groups. A. lumbricoides infection intensity declined 63.1% and 96.7% in the twice and three times per year treatment groups compared to the controls. T. trichiura infection intensity declined 40.4% and 75.9% respectively and hookworm intensity declined 35.3% and 57.2% respectively compared to control schools. These results suggest that school-based programmes can be a cost-effective approach for controlling the intensity of intestinal helminth infection even in environments where transmission is high.