A cross-sectional study was carried out to identify the association between diarrhea in 0-2 year-old children and children's characteristics, access to sanitation and housing conditions in a periurban area served by the Family Health Program, in the city of Guarulhos, SP. Data were obtained from FHP registration forms. Multiple logistic regression showed interaction for Housing*Sewage (other materials and non collected wastewater, p < 0.001), age group (4-9 months old, p = 0.054; 10 months and older, p = 0.008) as risk factors for diarrhea. Information collected by the Family Health Program could be an excellent tool to identify populations with poor housing and sanitation conditions at locations where sanitation indicators are not efficient to identify populations living at risk.