The aim of the present study was to compare the effects of guided tissue regeneration (GTR) with non-resorbable (ePTFE) and biodegradable barriers (Polyglactin 910). 23 patients provided 29 pairs of similar contralateral periodontal defects (12 pairs of interproximal intrabony lesions, 11 pairs of degree II and 6 pairs of degree III furcation defects). Each defect was randomly assigned to treatment with either non-resorbable (control [c]) or biodegradable (test [t]) devices. At baseline, 6, 12, 18, and 24 months after surgery, clinical measurements (PlI, GI, PPD, PAL-V, PAL-H) were performed. Standardized radiographs were obtained at baseline 12 and 24 months postsurgically. 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 [all defects: -2.97 +/- 1.90 mm (t), -2.21 +/- 1.73 mm (c); intrabony defects: -4.00 +/- 1.96 mm (t), -3.00 +/- 1.87 mm (c); degree II furcations: -2.67 +/- 0.97 mm (t), -2.08 +/- 1.54 mm (c)], PAL-V gain [all defects: 2.02 +/- 1.83 mm (t), 1.18 mm +/- 1.50 (c); intrabony defects: 3.45 +/- 1.48 mm (t), 1.95 +/- 1.64 mm (c); degree II furcations: 1.33 +/- 0.94 mm (t), 0.92 +/- 1.47 mm (c)], PAL-H gain [degree II furcations: 2.22 +/- 0.94 mm (t), 1.86 +/- 0.60 mm (c)], and radiographic changes [CEJ-AC: -0.56 +/- 1.98 mm (t), -0.06 +/- 1.19 mm (c); CEJ-BD: 2.10 +/- 1.92 mm (t), 1.24 +/- 2.04 mm (c)] after 24 months. For degree III furcations, neither statistically significant PPD reduction nor PAL-V gain was observed. Similar clinical and radiographic results were found 12 and 24 months after surgical treatment using either non-resorbable or biodegradable barriers. More favorable results concerning PAL-V gain in interproximal intrabony defects could be observed with biodegradable barriers after 24 months than using nonresorbable membranes. Whereas interproximal intrabony lesions and degree II furcation defects responded favorably to GTR therapy, through-and-through furcations must be looked upon as a contraindication for this regenerative technique. Based on the results of the present study, the use of biodegradable barriers in GTR may be recommended and, thereby, a surgical re-entry to remove nonresorbable barriers can be avoided.