This study reports the results obtained 36 months after treating deep periodontal defects with amelogenins. Results at 12 months have already been published. Sixteen of 21 patients completed the 3-year recall program. This study confirms after 3 years the results obtained at 1 year: Probing pocket depth decreased from 7.87 ± 2.03 mm to 2.93 ± 2.19 mm; recession increased from 2.20 ± 1.42 mm to 2.93 ± 1.87 mm; and attachment level decreased from 10.07 ± 2.28 to 5.87 ± 2.59 mm. No statistically significant difference was found between the data collected at 12 and 36 months. The standardized radiographs, digitized and analyzed with purpose-developed software, did not show any appreciable increase in bone volume, but only improved mineralization of the preexisting bone after 3 years using Emdogain without grafts.