The aim of the study was to evaluate the efficacy of dental caries prevention program with 3 years follow-up in children living in areas with fluoride and iodine deficiency. The study involved 625 school-aged children aged 6, 12 and 15 years receiving endogenous prevention with fluoridated and iodinated salt (300±50 mgF/kg and 40±10 mgI/kg). Enamel and dentine concentrations of CA, P, F and I were measured in 98 intact deciduous teeth by X-ray microanalysis before and after prevention program. Enamel and dentin microhardness was assessed in the same 98 teeth by Vickers Hardness Test. Obtained reduction of DMFT growth, positive changes of mineral composition and dental hard tissues microhardness prove high clinical efficacy of applied prevention program.