The hypothesis, a relationship between gingival tissue platelet activating factor (PAF) levels and healing after periodontal surgery, was tested by measuring PAF levels in gingival tissues collected from sites that had undergone flap surgery and guided tissue regeneration (GTR) or flap surgery alone. Using a split-mouth design, 20 intrabony defects were randomly assigned to treatment with flap surgery and GTR (group 1) or with flap surgery alone (group 2). Gingival tissue samples were obtained at surgery (baseline) and at 6-month follow-up evaluation visit. One half of each sample was used for analysis of PAF levels by high-performance liquid chromatography, and the other half of the sample was used for histomorphometric analysis that included measurements of number and diameter of blood vessels. PAF levels and diameter of blood vessels were significantly decreased (p < 0.01), and the number of blood vessels was significantly increased (p < 0.05) in both groups after 6 months compared to the baseline values. Postoperative number of blood vessels were significantly higher in group 1 (p < 0.05), whereas there was no significant difference in postoperative PAF levels between the two groups (p > 0.05). Based on the reported results, it is suggested that a decrease in gingival PAF levels might be found after conventional and regenerative periodontal surgery.