The changes in molecular composition of mixed saliva (oral fluid) were analyzed with the use of spectroscopic techniques for the patients with multiple caries. Using Fourier-transform infrared spectroscopy studies including synchrotron radiation for the excitation certain features were detected in the IR-spectra of the oral fluid. Mineral-organic, carbon-phosphate, AmidII/AmidI and protein/thiocyanate ratios were calculated for the groups of patients with multiple caries and patients of the control group. Complex analysis of the obtained experimental data enabled to determine that in the oral fluid of the persons with multiple caries as compared with the control group content of the mineral groups and complexes is reduced while the share of organic component is increased. Content of thiocyanate increases by more than two times and there appear carboxyl groups of esters, lipids and carbohydrates. The detected features in IR-spectra of mixed saliva as well as the changes found in its molecular composition based on the calculated ratios between organic and inorganic components can be used as biomarkers of cariogenic condition in the oral cavity. It can be used as a diagnostic criterion in the analysis of the oral fluid samples taken from the patients.