Purpose: To compare, by gene profiling analysis, the molecular events underscoring peri-implant mucosa formation at machined vs laser-microgrooved implant healing abutments. Materials and Methods: Forty endosseous implants were placed by a one-stage approach in 20 healthy subjects in nonadjacent sites for single-tooth restorations. In a split-mouth design, machined smooth and laser-microgrooved healing abutments were randomly assigned in each subject. Peri-implant mucosa adjacent to healing abutments was harvested by tissue punch biopsy at either 1, 2, 4, or 8 weeks following abutment placement. Total RNA was isolated from the peri-implant transmucosal soft tissues. A whole genome microarray using the Affymetrix Human Gene 2.1 ST Array was performed to describe gene expression profiles in relation to abutment topography and healing time duration. Data analysis was completed using GeneSpring software v.12.6. Results: Differential gene expression was revealed at all time points and among surfaces. Five hundred one genes were differentially expressed (fold change ≥ 2.0) at machined versus laser-modified abutments, and 459 of these were statistically significant (P ≤ .05). At 1 week, unique expression of IL-24 and MMP1 was observed in tissues from laser-treated surfaces. At 2, 4, and 8 weeks, mRNAs encoding keratins and protective proteins of cornified epithelium were upregulated in tissues from laser-modified abutments. At 4 weeks, upregulation (> 2-fold) of mRNAs encoding proteins associated with collagen fibril formation and function was observed in tissue from laser-modified abutments. In both tissues of machined and laser-modified abutments, mRNAs encoding junctional epithelium-specific proteins, ostogenic ameloblast associated protein (ODAM) and follicular dendritic cell secreted protein (FDCSP) were highly upregulated throughout weeks 2 to 8. Conclusion: Peri-implant abutment mucosal wound healing involves selective differentiation of epithelium and induction of the junctional epithelium. Laser-mediated alterations in abutment topography enhance collagen fibril-associated gene expression and alter epithelium/junctional epithelial gene expression. Clinically, shallower probing depths are measured at laser-mediated versus machined implant abutments. Keywords: dental implant abutment, junctional epithelium, laser, mucosal integration, titanium