The aim of the present study was to compare the effects of guided tissue regeneration (GTR) with non-resorbable (ePTFE [G]) and biodegradable barriers (Polyglactin 910 (V)). In 20 patients, providing 25 pairs of symmetrical periodontal defects (7 pairs of interproximal intrabony lesions, 12 pairs of degree II and 6 pairs of degree III furcation involvement), each defect was randomly assigned to treatment with either non-resorbable (control) or biodegradable (test) devices. At baseline and 6 months after surgery, clinical measurements (GI, PPD, PAL-V, PAL-H, P1I) and standardized radiographs were obtained. On the radiographs, the linear distances from the cemento-enamel junction (CEJ) to the alveolar crest (AC), and from the CEJ to bottom of the bony defect (BD) were measured using a computer-assisted analysing method (LMSRT). Both treatments revealed a significant (p < 0.05) PPD reduction (-2.90 +/- 1.33 mm (V), -2.71 +/- 1.41 mm (G)), PAL-V gain (1.78 +/- 1.27 mm (V), 1.46 +/- 1.35 mm (G)), PAL-H gain (2.00 +/- 0.82 mm (V), 1.60 +/- 0.59 mm (G)), and radiographic changes (CEJ-AC: 0.48 +/- 0.75 mm (V), 0.73 +/- 0.92 mm (G); CEJ-BD: -0.76 +/- 0.79 mm (V), -0.41 +/- 0.72 mm (G)) after 6 months. The mean differences between the changes for test and control were not significant for most clinical and radiographic parameters. Similar clinical and radiographic results were found 6 months after surgical treatment using either non-resorbable or biodegradable barriers. More favorable results concerning PAL-H gain could be observed with biodegradable barriers after 6 months. Therefore, based on these results, the use of biodegradable barriers in GTR may be recommended and, thereby, a surgical re-entry to remove non-resorbable barriers can be avoided.