The study aimed at evaluating the 2-year results obtained following combined surgical resective and regenerative treatment of advanced peri-implantitis defects comparing two methods of surface debridement/decontamination (DD). Twenty-four patients (n = 26 combined supra- and intrabony defects) completed the 24 months follow-up observation following access flap surgery, granulation tissue removal and implantoplasty at bucally and supracrestally exposed implant parts. The remaining aspects were randomly allocated to surface DD using either (i) an Er:YAG laser (ERL) device, or (ii) plastic curets + cotton pellets + sterile saline (CPS) were augmented with a natural bone mineral and covered with a collagen membrane. At 24 months, ERL treated sites failed to reveal significantly higher reductions in mean BOP (ERL: 75.0 ± 32.6% versus CPS: 54.9 ± 30.3%) and CAL values (ERL: 1.0 ± 2.2 mm versus CPS: 1.2 ± 2.2 mm) when compared with the CPS group. In both groups, mean CAL values were not significantly different when compared with baseline. The long-term stability of clinical outcomes obtained following combined surgical therapy of advanced peri-implantitis may be influenced by factors other than the method of surface debridement/decontamination. © 2012 John Wiley & Sons A/S.