The aim of the present study was to compare the efficacy of guided tissue regeneration (GTR) using two different biodegradable barriers (polylactide acetyltributyl citrate; polydioxanon) in three- and two-walled infrabony defects. The polydioxanon barrier is an experimental GTR membrane that consists of a continuous occlusive barrier with a layer of slings on the side that is meant to face the mucoperiosteal flap. Fifteen patients provided 15 pairs of similar contralateral periodontal defects: 12 predominantly two-walled and 18 predominantly three-walled infrabony defects. Each defect was randomly assigned to treatment with polylactide acetyltributyl citrate (control) or polydioxanon (test) devices. At baseline, 6, 12, 18, and 24 months after surgery, clinical measurements were performed and standardized radiographs obtained (not at 18 months). Both treatments revealed a significant Gingival Index reduction, probing depth reduction, and vertical probing attachment level gain 24 months after surgery. Both treatments showed slight resorption of the crestal alveolar ridge after 24 months, which failed to reach statistical significance. A statistically significant bone gain within the infrabony pockets was measured for both treatment options 24 months postsurgical. Regarding Gingival Index and probing depth reduction as well as vertical probing attachment level and bone gain, there were neither statistically significant nor clinically relevant differences between test and control barriers. The use of both biodegradable barriers in GTR therapy may be recommended.