Purpose: The structure of peri-implant soft tissue that is regenerated after flapless and flap surgery has been shown to differ. However, its underlying mechanisms are relatively unknown. The present study sought to identify differences in the inflammatory cell infiltration and expression of gene transcripts during transmucosal healing between the two approaches with two different implant designs. Materials and Methods: All mandibular premolars were removed from 12 minipigs. One month later, four implants (two NobelReplace Tapered Groovy and two NobelPerfect Groovy, Nobel Biocare) were placed in each quadrant. One quadrant was randomized to flapless insertion, while the other was chosen for flap surgery in each animal. Following 1, 2, 4, and 12 weeks of transmucosal implant healing, biopsy specimens were retrieved from the peri-implant soft tissue according to a standardized procedure to avoid crossover effects. Samples were subjected to a leukocyte count and a gene expression analysis. Results: When the flapless placement technique was used, leukocyte influx in the peri-implant soft tissue was significantly smaller compared to open surgery for both implant designs. Gene expression analysis revealed significant overexpression of molecules associated with detoxification and reepithelialization in the flapless group. In contrast, myofibroblast-associated gene transcripts were significantly enriched in the flap surgery group. Conclusions: The present data indicate perpetuation of inflammatory reactions as well as increased fibrotic scar tissue deposition in the peri-implant area following implant placement by the flap approach. Flapless implant insertion results in less inflammation and early reepithelialization, providing the potential for the formation of a fully functioning as well as esthetically preferable peri-implant soft tissue collar. Keywords: flapless surgery, soft tissue-implant interaction, wound healing