We evaluated the effect of annual ivermectin (IV) distribution for onchocerciasis on the prevalence of soil transmitted helminth (STH) infections in school-aged (SAC) and preschool-aged (PAC) children by comparing children in villages that had received treatment for 13 years to those from socioeconomically similar villages in untreated areas. We enrolled 1,031 SAC and 211 PAC for Kato Katz examinations. Treated areas had a lower prevalence of Ascaris (SAC: 3% versus 12%, P < 0.0001; PAC: 3% versus 10%, P < 0.051) and Trichuris (SAC: 6% versus 10%, P = 0.012; PAC: 1% versus 8%, P = 0.019), but not hookworm (SAC: 38% versus 42%, P = 0.20; PAC: 21% versus 27%, P = 0.30). The prevalence of Ascaris or Trichuris in treated areas was below the WHO threshold for mass antihelminthic treatment (MDA), but not for hookworm. We conclude that benzimidazole MDA in IV treatment areas is indicated to effectively control hookworm.