A cross-sectional study was carried out to determine the prevalence of Streptococcus mutans and Streptococcus sobrinus and the association of the two in a random sample (n=614) of the child population of the region of Valencia (Spain). Saliva samples were analyzed by the quantitative polymerase chain reaction (PCR) method to study the relation of these bacteria to caries prevalence and the DMFT index. The prevalence of S. mutans was 35.4% at age 12 and 22.9% at age 15, that of S. sobrinus 18.9% and 8.4% and that of the S. mutans-S. sobrinus association 18.2% and 6.8% respectively. At both 12 and 15 years of age, the caries prevalence rates were lower in the Streptococcus-free group of children (37.6% and 48.5% respectively) and higher in the S.mutans-only group (67.3% and 74.0%). At the age of 12, the DMFT index was significantly higher in the mutans-only carriers (2.1) than in the Streptococcus-free and S. mutans-S. sobrinus association groups (both 0.9). At the age of 15, the DMFT index was significantly higher in the S. mutans-S. sobrinus association (3.71) and mutans-only (3.1) carrier groups than in the Streptococcus-free group (1.4). Determination of S. mutans and S. sobrinus by real-time quantitative PCR can provide valuable information for caries risk assessment in epidemiological studies.