This study assessed the impact of adding community-directed treatment (ComDT) to the routine health facility (HF)-based treatment on prevalence and intensity of soil transmitted helminth (STH) infections among children aged 12 to 59 months. Repeated cross-sectional surveys were conducted among randomly selected children of this age group from the intervention area (HF+ComDT area) and the comparison area (HF area) at baseline (n=986), 12 months (n=796) and 18 months (n=788) follow-up. The prevalence of Ascaris lumbricoides was significantly higher in the HF+ComDT as compared to the HF area at baseline (P=0·048), but not at 12 and 18 months follow-up. At baseline the HF+ComDT area had significantly higher intensities of A. lumbricoides compared to the HF area (P<0·001), but not at 12 and 18 months follow-ups. Prevalence and intensity of hookworm did not differ significantly between treatment arms at any time. Analysis of trends showed a significant decrease in prevalence of A. lumbricoides and hookworm in the HF+ComDT area (P<0·001), of hookworm in the HF area (P<0·05), but not of A. lumbricoides in the HF area. It is concluded that the ComDT approach generally enhanced the treatment effect among under-five year children and that this alternative approach may also have advantages in other geographical settings.