Toll-like receptors (TLRs) are highly developed sensors to detect microbe-associated molecular patterns. Functional polymorphisms of the genes TLR4 and TLR9 were found to be associated with alveolar bone loss in a Porphyromonas gingivalis-induced periodontitis model in mice. Our aim was to examine whether such an association can be detected in a group of Finnish adults. Polymorphisms of TLR4 Asp299Gly (rs4986790) and TLR9 rs187084 (1486 T/C) were genotyped by pyrosequencing and PCR from the saliva samples of 223 adults (age range 40-60 years). Alveolar bone loss, measured from panoramic radiographs, were compared between TLR genotype groups according to subjects' salivary carriage of P. gingivalis, measured using a single copy gene-based real-time PCR. The frequencies of TLR4 wild type and heterozygote variants were 87.4 % and 12.6 %, respectively, while those of TLR9 wild type, heterozygote, and homozygote variants were 25.6 %, 39.1 %, and 35.3 %, respectively. In the TLR4 heterozygote group, P. gingivalis-positive subjects had more alveolar bone loss than P. gingivalis-negative subjects (p = 0.027), while no difference was observed in the wild type group. P. gingivalis-negative individuals with TLR9 heterozygotes exhibited significantly less alveolar bone loss compared to those with TLR9 wild type (p = 0.007). Polymorphisms of TLR4 in P. gingivalis carriers seem to expose to alveolar bone loss. Polymorphisms of TLR9 can be protective against alveolar bone loss in the absence of P. gingivalis.