Soil-transmitted helminth (intestinal worm) infections are very common in developing countries and are an important cause of illness. Mass de-worming treatments of school children are an important strategy to reduce illness caused by these infections in communities without access to clean water and sanitation. Few studies have examined the effect of repeated mass treatments in the long-term in controlling these infections. The objective of the present study was to assess the impact of the drug ivermectin used for the control of onchocerciasis (river blindness), that has important effects against intestinal worms, on the epidemiology of intestinal worms in children when administered repeatedly for 15–17 years. We compared the epidemiology of infections between children living in communities that received ivermectin with communities that never received the drug. The data suggest that ivermectin has important differential effects on intestinal worms with a greater impact on infections with Trichuris trichiura and little impact on Ascaris lumbricoides and hookworms infections. Our data suggest that long-term ivermectin treatments may provide health benefits through effects on T. trichiura infections but that the addition of second de-worming drug such as albendazole may be required for the control of other intestinal worm infections.