An awareness of the presence of cardiovascular disease risk factors since childhood is essential to guide health promotion policies. The aim of this paper is to present, together with the main results, a methodological proposal to estimate both incidence and prevalence of these factors over time and their associated socio-demographic aspects in a population attending a primary health care unit, within Brazilian Unified National Health System. An open cohort design was adopted, starting in 2004 with a sample of 356 children aged between 5 and 9. In the second wave, in 2008, 126 children were enrolled and 205 were reevaluated. Socioeconomic variables, food intake, physical activity, anthropometric measures (weight, height and waist size), lipidogram and glycemia were collected. Results indicate a high prevalence of dyslipidemia, and an increase of excess weight and sedentary activity between both surveys. Some 55% of children were found to have lower values of HDL-cholesterol. The methodological proposal was considered adequate for the monitoring of cardiovascular disease predictors in poor urban populations.