miRNA molecules have been attracting attention as genetic modifiers between organs. We examined the relationship between serum miRNA and targeted liver mRNA profiles in a periodontitis rat model, and the influence of periodontitis on the liver.Male Wistar rats (n=16, 8 weeks old) were randomly divided into two groups (8 rats each): control and periodontitis (ligature placement for 4 weeks). Serum miRNA and liver mRNA profiles were compared.Periodontal destruction and hepatocyte apoptosis were induced in the periodontitis group. Microarray analysis indicated that 52 serum miRNAs and 33 liver mRNAs were expressed with a >1.5-fold change (FC) and a >2.0-FC (p<0.05), respectively, between the two groups. From the miRNA target genes, 12 genes equivalented to liver mRNAs with a >2.0-FC, among which, Hyou1, Chac1, and Bloc1s3 have apoptotic functions in our model. miRNAs upstream of these 3 mRNAs are miR-3591, miR-181a-2-3p and miR-6321.miR-3591, miR-181a-2-3p and miR-6321 induced hepatocyte apoptosis in our periodontitis rat model.