OBJECTIVE The aim of the present study was to identify the free amino acid content in whole saliva of children with (CE) and without early childhood caries (CF) (ECC), correlating these findings with caries experience and mutans streptococci (MS) levels in saliva. METHODS Seventy-eight healthy children, both genders, 6-71 months age, were selected to participate in the study. Following examination for dmft scores calculation, unstimulated whole saliva was collected from all 78 participants, stored at -80 degrees C, and used for amino acid analysis, on a Biochem 20 plus amino acid analyzer. Stimulated whole saliva was collected from 52 children, transported, diluted and plated on MSB agar medium for detection of MS in cfu/mL. RESULTS Forty different free amino acids were identified in whole saliva, with great variation in their concentration. A statistically significant relation was found between caries experience and the presence of free proline and glycine. While proline (p=0.0182) was more frequently absent in the CF group, the absence of glycine (p=0.0397) was more often observed in the CE group. In the presence of higher levels of MS, free glycine reduced the risk of experiencing dental caries (p=0.0419). Conversely, the presence of proline was found to increase the risk of experiencing the disease (p=0.0492). CONCLUSIONS The presence of free proline and absence of free glycine in children with ECC, highly contaminated with MS, increased the chances of experiencing dental caries in the present population. Further studies are needed to better understand this phenomenon.