In 16 patients with advanced periodontitis, 23 teeth exhibiting interproximal intrabony defects were treated by conventional periodontal surgery (n = 10, control) or guided tissue regeneration (GTR) technique using expanded polytetrafluoroethylene (ePTFE) barriers (n = 13, test), respectively. Clinical parameters were assessed before and 6 months after surgery. Presurgically and 3 and 6 months postsurgically standardized bite-wing radiographs were taken. Using a loupe and a computer-assisted system, respectively, the distances from the cemento-enamel junction (CEJ) to alveolar crest (AC) and CEJ to the most apical extension of bony defect (BD) were measured. The average gain of attachment was assessed 2.33 mm in the control group and 3.17 mm in the test group. The bony fill was measured 0.97 mm and 0.97 mm in the control group and 0.93 mm and 1.68 mm in the test group after 3 and 6 months, respectively, using a loupe. Using a computer-assisted system 0.83 mm and 1.82 mm of bone fill could be measured (control) and 0.76 mm and 1.79 mm (test) after 3 and 6 months, respectively. Compared to the gold standard of surgical measurements, the computer-assisted analysis of radiographs underestimated bone loss significantly less than evaluation with a loupe (P < 0.002). Compared to conventional periodontal surgery, the GTR technique resulted in higher attachment gain and bony fill. However, the high variation of surgical results in the test group prevented the calculation of a statistically significant difference.