Many latrine campaigns in developing countries fail to be sustained because the introduced latrine is not appropriate to local socio-economic, cultural and environmental conditions, and there is an inadequate community health education component. We tested a low-cost, locally designed and constructed all-weather latrine (the “BALatrine”), together with community education promoting appropriate hygiene-related behaviour, to determine whether this integrated intervention effectively controlled soil-transmitted helminth (STH) infections. We undertook a pilot intervention study in two villages in Central Java, Indonesia. The villages were randomly allocated to either control or intervention with the intervention village receiving the BALatrine program and the control village receiving no program. STH-infection status was measured using the faecal flotation diagnostic method, before and eight months after the intervention. Over 8 months, the cumulative incidence of STH infection was significantly lower in the intervention village than in the control village: 13.4% vs. 27.5% (67/244 vs. 38/283, p < 0.001). The intervention was particularly effective among children: cumulative incidence 3.8% (2/53) for the intervention vs. 24.1% (13/54) for the control village (p < 0.001). The integrated BALatrine intervention was associated with a reduced incidence of STH infection. Following on from this pilot study, a large cluster-randomised controlled trial was commenced (ACTRN12613000523707).