In 24 patients with advanced periodontitis 38 interproximal intrabony defects were treated by conventional surgery (C; n = 8) or guided tissue regeneration (GTR) using expanded polytetrafluoroethylene (G; n = 17) or Polyglactin 910 barriers (V; n = 13). Presurgically (BL), 6 and 12 months postsurgically clinical parameters (GI, PII, PPD, PAL-V) and 36 standardized radiographs were obtained generating 72 pairs (36 BL/6 months; 36 BL/12 months). Using linear measurements on the radiographs and subtraction analysis, bony fill within the defects was assessed. Intrasurgically the extension of the intrabony defects was measured. Statistically significant (p < 0.05) attachment gain was found after 6 (C: 2.4 +/- 1.6 mm; G: 3.2 +/- 1.6 mm; V: 3.4 +/- 1.5 mm) and 12 months in all groups (C: 2.4 +/- 1.7 mm; G: 3.1 +/- 1.7 mm; V: 4.0 +/- 1.7 mm). Thirty-nine of 72 pairs of radiographs were unsuitable for subtraction analysis. Significant (p < 0.05) bony fill was observed at 6 (C: 0.3 +/- 1.0 mm; G: 0.7 +/- 1.2 mm; V: 0.9 +/- 1.2 mm) and 12 months (C: 0.0 +/- 1.1 mm; G: 1.4 +/- 1.5 mm; V: 1.5 +/- 1.7 mm) only after GTR surgery. GTR therapy yielded significantly more bony fill than conventional surgery 12 months postsurgically (p < 0.1). Bony fill (linear measurement) was influenced by age, smoking, baseline bone loss and PAL-V gain (p < 0.0001). Significantly more radiographs taken with potentially unstable support of the filmholder were not suitable for subtraction analysis than those with stable support (p < 0.05). Bony gain (subtraction analysis) was positively modulated by bony fill (linear measurement) and use of biodegradable barriers (p = 0.002). There is a correlation between PAL-V gain and bony fill (linear measurement). Smoking impairs attachment gain and bony fill. Potentially stable support of the filmholder provided radiographs suitable for subtraction analysis.