The purpose of this randomized clinical trial was to compare the clinical outcome of two different surgical approaches for the treatment of peri-implantitis. Seventeen patients with ITI(R) implants were included consecutively over a period of 5 years. The patients were randomized with a lottery assignment. Ten patients were treated with resective surgery and modification of surface topography (test group). The remaining seven patients were treated with resective surgery only (control group). Clinical parameters (suppuration, modified plaque index - mPI, modified bleeding index - mBI, probing pocket depth - PPD, pseudopocket - DIM, mucosal recession - REC, probing attachment level - PAL) were recorded at baseline, as well as 6, 12, 24 and 36 months after treatment. The cumulative survival rate for the implants of the test group was 100% after 3 years. After 24 months, two hollow-screw implants of control group were removed because of mobility. Consequently, the cumulative survival rate was 87.5%. The recession index in the control group was significantly lower than in the test group at 24 months (Student's t-value of -2.14). On the contrary, control group showed higher PPD, PAL and mBI indexes than test group (Student's t-values of +5.5, +2.4 and +9.61, respectively). The PPD and mBI indexes for the implants of the control group were significantly higher at baseline than 24 months later (Student's t-values of +3.18 and +3.33, respectively). Recession and PAL indexes resulted in values significantly lower than baseline (Student's t-values of -4.62 and -2.77, respectively). For the implants of the test group PPD and mBI indexes were significantly higher at baseline than 36 months after (Student's t-values of +11.63 and +16.02, respectively). Recession index resulted in values significantly lower at baseline (Student's t-value of -5.05). No statistically significant differences were found between PAL index measurement at baseline and 36 months later (Student's t-value of +0.89). In conclusion, resective therapy associated with implantoplasty seems to influence positively the survival of oral implants affected by inflammatory processes.