BACKGROUND Mutans streptococci (Streptococcus mutans and S. sobrinus) are considered to be major etiologic agents of dental caries. Using a polymerase chain reaction method, we detected those bacteria from 145 outpatients (6-30 years old) with intellectual disabilities (ID) and their presence was compared with the incidence of dental caries. METHODS Plaque samples were collected from all erupted tooth sites in subjects with a sterile toothbrush. A dental examination was performed to determine the number of decayed and filled teeth (DFT score) in permanent dentition using the WHO caries diagnostic criteria. A Mann-Whitney U-test was employed to compare the caries scores between combinations of the bacteria, and with a Wilcoxon rank test used to compare caries scores between the baseline and after 1 year. RESULTS Among all subjects, S. mutans and S. sobrinus were possessed by 78.7 and 83.5%, respectively, while 13.1% were positive for S. mutans alone, 17.9% for S. sobrinus alone, and 65.6% for both organisms, with 3.4% were negative for both. The mean DFT score of subjects positive for both S. mutans and S. sobrinus at after 1 year was significantly higher than that of those positive for S. mutans alone (P < 0.01). The increase in caries increment was also significantly greater in subjects with both bacteria detected (P < 0.001). CONCLUSIONS Our results indicate that patients with ID harboring both S. mutans and S. sobrinus have a significantly higher incidence of dental caries than those with S. mutans alone.