Objectives: 1) To determine the phenotypic response of all F2 mouse population progenies to periodontitis by microCT analysis. 2) To perform genome wide search for QTL associated with host susceptibility to periodontitis. Methods: 408 mice of F2 population were generated from the two parental inbred lines. Infection was performed with Porphyromonas gingivalis and Fusobacterium nucleatum. Six weeks following the final infection, alveolar bone loss was quantified using microCT. Genomic DNA of the phenotypic extremes (38%) was genotyped with 170 SNP markers, covering the mouse genome and subsequently performing QTL mapping analysis. Results: The mean phenotypic response of F2 population was found to be intermediate between the two parental founders. Analysis results suggested no significant sex effect. Two highly significant QTL were identified and mapped on chromosomes 3 and 5. Conclusions: This is the first report to map QTL associated with host susceptibility to periodontitis in mice. Our next step is to identify Candidate genes underlying these QTL.