OBJECTIVE Guided tissue regeneration has been shown to lead to periodontal regeneration, however, the mechanisms involved remain to be clarified. The present study was carried out to assess the expression of genes involved in the healing process of periodontal tissues in membrane-protected vs. nonprotected intrabony defects in humans. METHODS Thirty patients with deep intrabony defects (> or = 5 mm, two or three walls) around teeth that were scheduled for extraction were selected and randomly assigned to receive one of the following treatments: flap surgery alone (control group) or flap surgery plus guided tissue regeneration (expanded polytetrafluorethylene (e-PTFE) membrane) (test group). Twenty-one days later, the newly formed tissue was harvested and quantitatively assessed using the polymerase chain reaction assay for the expression of the following genes: alkaline phosphatase, receptor activator of nuclear factor-kappa B ligand, osteoprotegerin, osteopontin, osteocalcin, bone sialoprotein, basic fibroblast growth factor, interleukin-1, interleukin-4, interleukin-6, matrix metalloproteinase-2 and matrix metalloproteinase-9. RESULTS Data analysis demonstrated that mRNA levels for alkaline phosphatase, receptor activator of nuclear factor-kappa B ligand, osteoprotegerin, osteopontin, bone sialoprotein, basic fibroblast growth factor, interleukin-1, interleukin-6, matrix metalloproteinase-2 and matrix metalloproteinase -9 were higher in the sites where guided tissue regeneration was applied compared with the control sites (p < 0.05), whereas osteocalcin mRNA levels were lower (p < 0.05). No difference was observed in interleukin-4 mRNA levels between control and test groups. CONCLUSIONS Within the limits of this study, it can be concluded that genes are differentially expressed in membrane barrier-led periodontal healing when compared with flap surgery alone, and this may account for the clinical outcome achieved by guided tissue regeneration.