The aim of this study was to evaluate the risk factors associated with the occurrence of caries in permanent teeth (PT) and in the permanent first molar (PFM) seven years after their eruption. Children born in 2005 who were enrolled in a Community Dental Program were included. A total of 278 children were enrolled. Evaluated risk factors were parental caries experience, educational level of the mother, routine medications, systemic diseases, dietary habits, toothbrushing frequency, existence of molar incisor hypomineralization (MIH) in the PT, and caries in the temporary teeth (TT). Associations between independent variables and the DMF-T (decayed, missing, and filled teeth in PT) and DMF-M (DMF in PFM) indices, only considering cavitated and non-cavitated carious lesions or cavitated carious lesions as outcomes, were evaluated by Poisson regression with robust variance analysis. A cariogenic diet (sweets and soft drinks), toothbrushing frequency of <1 a day, a presence of df-t (decayed and filled temporary teeth) score of >0, low educational level of the mother, and existence of MIH were associated with high DMF-T or DMF-M values (p < 0.05). We can conclude that the intake of sweets and soft drinks, toothbrushing frequency, the presence of caries in TT, and MIH in PT were the best predictors of the occurrence of caries in PT and PFM.