The purpose of this study was to determine the effect of use of an absorbable collagen membrane in guided tissue regeneration (GTR) therapy upon the subgingival microflora. The study group consisted of 12 systemically healthy patients with bilateral mandibular furcation defects with attachment loss > or = 6 mm; one site was randomly assigned for GTR treatment while the contralateral site received surgical flap debridement only. Subgingival plaque samples were collected by paper point on the day of surgery and at 2, 4 and 6 months post-surgery. Three sites were sampled in each patient: a collagen membrane site, a control surgical site, and an unoperated control site. Plaque samples were transported in a non-phosphated buffer solution and examined by phase-contrast microscopy. Cocci, rods, spirochetes, fusiforms, curved rods, and total bacteria were recorded per 10 high-power fields. Following statistical analysis utilizing the Bonferroni (Dunn) t test, no differences in total bacterial counts were found among the sites at any of the time intervals examined. Total bacterial counts were found lower at both the collagen membrane and control surgical sites post-surgery as compared to unoperated control sites, but these differences were not statistically significant (P > .05). In addition, no significant differences were detected in bacterial profiles between sites or individual time points. Results from this 6-month limited clinical trial suggest that the placement of an absorbable collagen membrane as part of a standard surgical regimen for GTR therapy does not alter the local microflora.