OBJECTIVE: To estimate the incidence of congenital syphilis and identify its relationship with Family Health Strategy coverage. METHODS:An observational ecological study was carried out with both descriptive and analytical components, by two different approaches: one that explores a temporal series (2003 to 2008) RESULTS:Increasingly trends of congenital syphilis notifi cation in Brazil refl ect social inequalities in the distribution of cases. The incidence of congenital syphilis was lower in the municipalities with high Family Health Strategy coverage; however, after controlling for the co-variables, such an effect might be attributed to the coverage of prenatal care and the demographic characteristics of the municipalities where the implementation of the Strategy was a priority. CONCLUSIONS:Despite the increase in prenatal care coverage, the actions implemented still exhibit low effectiveness in the prevention of congenital syphilis. Prenatal care performed by Family Health Strategy teams did not control syphilis better than the prenatal care performed within the context of other models of assistance.