Objective. To study the correlation between the level of infection with Streptococcus mutans (SM) and lactobacilli (LB) in saliva with existing status and the development of primary dental caries in 3-year-old children and to evaluate the results of CRT® bacteria as a Caries Risk Test. Methods. A total of 140 3-year-old children were selected for the study. Oral examination was conducted and the levels of infection with SM and LB in saliva were measured using a CRT® bacteria test. Oral reexamination was conducted after two years. The prevalence rate of caries, the decayed-missing-filled tooth (dmft) and decayed-missing-filled surface (dmfs) indices, and Caries Severity Index (CSI) were calculated at the start and end of the two years. The indices were statistically analyzed. Results. The caries prevalence rate, dmft, dmfs, and CSI increased with increasing levels of CRT-SM and CRT-LB at the start and end of the two years; the increases in dmft, dmfs, and CSI over the period were consistent with the increases in CRT-SM and CRT-LB levels, with all differences being highly statistically significant. The increase in caries prevalence rate over the two years was not statistically different for different CRT-SM and CRT-LB levels. CRT-SM and CRT-LB levels were highly positively correlated with dmft, dmfs, CSI and their increases over the two years. Levels of infection with oral SM and LB were found to be independent risk factors for primary dental caries, respectively. For an SM concentration in saliva of ≥104 CFU/mL and an LB concentration of <104 CFU/mL, the risk of caries increased by approximately 2.8-fold. When the concentration of LB in saliva was ≥104 CFU/mL and that of SM <104 CFU/mL, the risk of caries increased by approximately 3.9-fold. When the concentration of both SM and LB was ≥104 CFU/mL, the risk increased by approximately 10.9-fold. Conclusions. Significant positive correlations were found between the level of infection with oral SM and LB and existing oral decay status and the trend in the development of primary dental caries. Infection with SM and LB significantly increased the risk of caries in primary teeth. The CRT® bacteria is a simple, convenient, reliable, and effective Caries Risk Test.