BACKGROUND As dietary management during early childhood is a great barrier in caries control, there is a need for the identification of intrinsic risk factors, capable of allowing the use of a more cost-effective approach to early childhood caries (ECC). OBJECTIVE To evaluate the salivary peptide profile of children with and without ECC and its association with caries experience. METHODS One hundred and six 10- to 71-month-old children participated in the study. Caries experience was determined through the visual/tactile method, based on the number of decayed, missing, and filled teeth, and surface scores (dmft/dmfs). Whole saliva was collected for mutans streptococci (MS) detection and peptide analysis. RESULTS Chromatograms from CF (children without caries experience, n = 58) and CE (children with caries experience, n = 48) saliva pools expressed different patterns. Identification of molecular masses suggested the presence of nine peptides. Three of them were significantly related with caries experience. HNP-3 (α-defensin 3) (P = 0.019) and HBD-3 (β-defensin 3) (P = 0.034) reduced the chances of experiencing ECC. Proline-rich peptides IB-4 significantly increased caries experience (P = 0.035). Age (P = 0.020) and MS counts (P = 0.036) increased caries experience; however, gender was not associated with dental caries (P = 0.877). CONCLUSIONS Specific salivary peptides of CF or CE children in early childhood predispose to a higher or lower risk of caries experience.