Purpose: Many histologic and histomorphometric studies as well as systematic reviews have shown the clinical success of the use of anorganic bovine bone (ABB, Bio-Oss) in maxillary sinus floor augmentation (MSFA). The molecular processes involved in bone healing are, however, still unknown. The aims of this study were to explore gene expression associated with bone remodeling and inflammation in MSFA sites. Materials and Methods: The mRNA expression levels of runt related transcription factor 2 (RUNX2), receptor activator of NF-kB ligand (RANKL), osteoprotegerin (OPG), matrix metallopeptidase 9 (MMP-9), tartrate-resistance acid phosphatase (TRAP), and interleukin-1beta (IL-1β), as well as the ratio of RANKL/ OPG were compared between alveolar bone of a group after MSFA with ABB and a maxillary posterior edentulous bone group. Twenty-one bone samples were collected at the time of implant placement after 6 months of MSFA or tooth extraction. Fourteen bone samples from the MSFA group and from the maxillary posterior edentulous bone without MSFA group were taken to analyze gene expression by real-time reverse transcription polymerase chain reaction (RT-PCR). Seven bone samples from the MSFA group were used for histologic analysis. Results: Real time RT-PCR revealed no statistically significant difference in gene expression level of RUNX2, RANKL, OPG, MMP-9, TRAP, and IL-1β, or in the ratio of RANKL/OPG. Histology showed bone-lining cells at the edge and osteocyte inside newly formed bone. Residual grafted particles were in close contact with new bone. Conclusion: After a healing period of 6 months, ABB particles did not have an effect on the expression of genes associated with bone remodeling and inflammation. In addition, histologic evidence supports that ABB particles are replaced by new bone formation and do not affect bone healing. Keywords: gene expression, histology, histomorphometry, maxillary sinus floor augmentation, real-time RT-PCR, xenograft