The aim was to investigate the influence of Streptococcus mutans on the level of immune system biomarkers in oral fluid in children for further development of highly accurate prediction methods for dental caries. 398 children were examined, aged between 3 and 15 years, who were divided into two groups. The research group (L1) 132 children with caries lesions and 266 caries-free children formed the control group (L0). The number of Streptococcus mutans, the level of tumor necrosis factor alpha (TNF-ɑ), transforming growth factor beta-1 (TGF-β1), secretory immunoglobulin A (sIgA) and antimicrobial peptide (cathelicidin LL-37) were estimated in oral fluid (OF). The positive test result determined the increased number of Streptococcus mutans in OF of > 5x105 CFU/mL was estimated at 53.0%, p < 0.001 of children in L1 and 8.6% of subjects in L0, which indicates an increased risk of developing carious lesions in the future. The low number of Streptococcus mutans in OF of < 5x105 CFU/mL was appreciated and the patient does not show a risk of developing carious lesions in the future. Conclusions:Children with increased numbers of Streptococcus mutans in the OF (>5x105 CFU/mL) were found to have statistically significant increases in the number of demineralized areas of tooth enamel, compared to subjects with low numbers of Streptococcus mutans in the OF (<5x105 CFU/mL). The comparative study of immune system biomarkers showed deficient level of salivary protective factors: sIgА, LL-37 and TGF-β1 and significantly increased level of TNF-α in children with high number of Streptococcus mutans.