The aim of the present clinical trial was to compare the long-term effect of EMDOGAIN treatment as an adjunct to modified widman flap (MWF) surgery with the effect of MWF and placebo treatment. The investigation was a placebo-controlled, randomized multicenter trial involving 33 subjects with 34 paired test and control sites. The protocol required 2 interproximal sites, appropriately separated, in the same jaw with probing pocket depths > or = 6 mm and an associated intrabony defect with a depth of > or = 4 mm and a width of > or = 2 mm as measured on a radiograph. Only predominantly 1- and 2-wall defects were included. Clinical attachment gain and radiographic bone gain were used as primary outcome variables. Assessments were made at baseline, 8, 16 and 36 months. Mean values for clinical attachment level gain in test and control sites at 8 months were 2.1 mm and 1.5 mm, respectively; at 16 months, 2.3 mm and 1.7 mm, respectively; and at 36 months 2.2 mm and 1.7 mm, respectively; and the differences were statistically significantly different at each time point (p < 0.01). The radiographic bone level continued to increase over the 36 months at the EMDOGAIN-treated sites, while it remained close to the baseline level at the control sites. The statistically significant (p < 0.001) radiographic bone gain at 36 months of 2.6 mm at EMDOGAIN-treated sites corresponded to 36% gain of initial bone loss or 66% defect fill. The present trial has demonstrated that topical application of EMDOGAIN onto diseased root surfaces associated with intrabony defects during MWF periodontal surgery will promote an increased gain of radiographic bone and clinical attachment compared to control (placebo application) surgery in the same patient. There was no evidence to indicate any clinical adverse effects from application of EMDOGAIN conjunction with periodontal surgery.