The aim of this controlled retrospective study was to evaluate the influence of an IL-1 gene polymorphism on the clinical and radiographic healing outcomes of GTR therapy. The study included 47 adult periodontitis patients with 94 deep intrabony defects treated by GTR using different membrane materials. The following clinical parameters were recorded at baseline and 12 months after surgery: papillary bleeding index (PBI), gingival recession (REC), probing pocket depth (PPD), clinical attachment level (CAL), and the vertical relative attachment gain (V-rAG). Bone changes in the defect regions due to GTR therapy were quantitatively evaluated using digital subtraction radiography (DSR). Polymorphisms of the IL-1A gene at position - 889 and of the IL-1B gene at position + 3953 were analyzed by PCR. Statistical analysis was performed using the Mann-Whitney-U and the Wilcoxon-Signed-Rank tests (alpha = 0.05). The study comprised 19 IL-1 genotype positive (IL-1 +) patients and 28 IL-1 genotype negative (IL-1 -) patients. Twelve months after GTR therapy, both patient groups revealed statistically significant PPD reductions and CAL gain [median (25/75% percentiles)]: Delta PPD [IL-1 + : 4.0 (2.5/5.0) mm; IL-1-: 3.8 (3.0/4.9) mm], Delta CAL [IL-1 + : 3.5 (3.0/4.8) mm; IL-1 -: 3.0 (1, 2/4, 5) mm]. V-rAG amounted to 60.0 (47.7/78.6)% in IL-1 + patients and 53.1 (43.4/81.9)% in IL-1 - patients. Both patient groups showed significant bone density gain in 40% (IL-1 +) and 43.6% (IL-1 -) of the initial defect area due to GTR. Neither the clinical nor the radiographic healing parameters revealed any statistically significant differences in the GTR healing outcome between IL-1 + and IL-1 - patients. In conclusion, these 12-month findings indicate that the IL-1 gene polymorphism has no influence on the clinical and radiographic regeneration results following GTR therapy.