Objective: to compare the concentration and serotype of Streptococcus mutans in saliva of Down syndrome (DS), mental retarded (MR) and healthy control (C) individuals of the Región Metropolitana Sur of Santiago of Chile. Design of the study: Hundred and seventy nine male and females children and adolescents, aged between 5 to 19 years, 59 DS, 60 MR and 60 C were studied. Saliva samples were cultured in TYCSB agar for quantification, biochemical and serological tests. ANOVA and Chi-square for homogeneity tests were applied. Results: C, DS and MR presented Streptococcus mutans (serotypes c, e, f) and Streptococcus sobrinus (d, g, h), but only among DS and MR non-typifiable (No-tip) Streptococcus mutans were found. MR and DS showed higher bacteria concentration scores than C (P=0.001). Serotypes showed a significant heterogeneity of concentration scores: d, g, h showed the highest and No-tip the lowest one (P = 0.037). Conclusions: No-tip bacteria were absent in C and present in MR and DS; this result indicates different immune and ecological conditions among these human groups. The score of Streptococcus mutans in saliva was higher in DS and MR than in C.