Purpose: To evaluate the gene expression levels of semaphorins 3A, 3B, 4A, and 4D in both healthy and diseased implants. Materials and Methods: Subjects with peri-implantitis presented clinical attachment loss, probing depth ≥ 5 mm, bleeding on probing and/or suppuration, and radiographic bone loss > 4 mm. Peri-implant tissue biopsy specimens were sampled for analysis of the mRNA expression levels for semaphorins 3A, 3B, 4A, and 4D. A real-time polymerase chain reaction was performed, and the gene expression levels of semaphorins in relation to the housekeeping gene were analyzed by using the nonparametric Mann-Whitney test (P .05). Results: Thirty-five subjects (16 men, 19 women; mean age: 54.12 ± 2.34 years) with implant-supported restorations, using screw-shaped dental implants with internal or external hexagon were enrolled in this study. Higher levels of semaphorins 3A and 4D were detected in the peri-implantitis compared with the healthy tissues (P = .0011 and P = .0404, respectively), whereas Sem4A levels were significantly higher in the control group (P .0001). Differences between groups in the expression levels of Sem3B were not significant. Conclusion: Advanced peri-implantitis lesions showed higher levels of gene expression for Sem3A and Sem4D and lower levels of Sem4A in comparison to tissues obtained from a healthy dental implant. Keywords: dental implants, gene expression, peri-implantitis, real-time PCR, semaphorins