© 2019 Nomura et al. Aim: Evaluation of tooth surface level effect of cariogenic bacteria and sealant. Background: International Caries Detection Assessment System (ICADS) is a clinical scoring system that can assess the non-cavitated early stage of dental caries by surface level. Scores used in ICDAS are ordinary and each tooth within one individual is not statistically independent. Objective: In this study, by applying mixed effect modeling, the effect of cariogenic bacteria and fissure sealant for tooth surface-level caries progression was analyzed. Methods: Ninety-eight patients who had been regularly visited the dental hospital for the regular check-ups were enrolled in this study. Among them, patients who visited at baseline, after one and two years, were included for the analysis. Fifty-two patients were dropped out. The study population consisted of 25 boys and 21girls and their mean ages were 9.3 +/-2.1. Salivary levels of cariogenic bacteria were measured by qPCR. Mixed effect modeling with repeated measures was applied for the analysis. Results: Salivary levels of S. mutans and Lactobacilli were affected by the progression of the ICDAS score. Maxillary teeth, molars and buccal and occlusal surfaces were tended to progress. Maxillary tooth, molar tooth and buccal, approximal, and occlusal surface were tended to be affected by both cariogenic bacteria. Conclusion: By applying mixed effect modeling, highly-detailed surface-level analysis can be available.