The purpose of this prospective study was to assess the outcome of periradicular surgery with or without guided tissue regeneration (GTR) for the treatment of through-and-through lesions. Thirty-four teeth were included according to specific selection criteria. In the test group (using GTR), after root-end filling, the defects were filled with anorganic bovine bone and covered with a resorbable collagen membrane. Healing was assessed according to specific criteria and graded as successful, doubtful, or failed. In the control group, neither grafts nor membranes were used. After 1 year, 31 teeth were evaluated. Of these, 22 (71%) healed successfully, 6 (19%) showed doubtful healing, and 2 were recorded as failures. The outcomes of the defects treated with GTR (88% successful) were significantly better than those of the control group (57% successful). The present study showed that the use of GTR associated with anorganic bovine bone in the treatment of through-and-through lesions may positively affect the healing process.