Purpose: Implant placement entails disruption of the epithelial continuity, which can lead to various complications. Therefore, the area of mucosal penetration is of particular interest clinically. The goal of the present study was to compare gene expression in peri-implant soft tissue (PIST) with that in oral mucosal tissue (OMT) using microarray analysis, and to investigate which genes were specifically expressed in PIST. Materials and Methods: The bilateral upper first molars were extracted from 4-week-old rats and titanium alloy implants placed only in the left-side extraction sockets. Four weeks after surgery, samples were harvested from the left-side PIST and right-side OMT and total RNA samples isolated. Microarray analysis was used to compare gene expression in PIST and OMT, which was then confirmed using quantitative realtime polymerase chain reaction. Immunohistochemical staining was also performed to confirm protein level expression. Results: The number of genes expressed with more than a twofold change in PIST compared with OMT was 1,102, of which 750 genes were upregulated and 352 genes were downregulated. The messenger RNA (mRNA) expression of three selected genes-CEACAM1, IFITM1, and MUC4-were more significantly expressed in PIST than in OMT(P .01). Immunohistochemical localization of CEACAM1, IFITM1, and MUC4 was observed in PIST, but no immunoreaction was recognized in OMT. Conclusion: The result of microarray analysis showed that, because of implant placement, 750 genes were upregulated in PIST compared with OMT. CEACAM1, IFITM1, and MUC4 were specifically upregulated in PIST. Keywords: dental implant, microarray analysis, oral mucosal tissue, peri-implant soft tissue