Background: The guided bone regeneration (GBR) technique is highly successful for the treatment of peri-implant bone defects. The aim was to determine whether or not implants associated with GBR due to peri-implant defects show the same survival and success rates as implants placed in native bone without defects. Material and Methods: Patients with a minimum of two submerged dental implants: one suffering a dehiscence or fenestration defect during placement and undergoing simultaneous guided bone regeneration (test group), versus the other entirely surrounded by bone (control group) were treated and monitored annually for three years. Complications with the healing procedure, implant survival, implant success and peri-implant marginal bone loss were assessed. Statistical analysis was performed with non-parametric tests setting an alpha value of 0.05. Results: Seventy-two patients and 326 implants were included (142 test, 184 control). One hundred and twenty-five dehiscences (average height 1.92±1.11) and 18 fenestrations (average height 3.34±2.16) were treated. At 3 years post-loading, implant survival rates were 95.7% (test) and 97.3% (control) and implant success rates were 93.6% and 96.2%, respectively. Mean marginal bone loss was 0.54 (SD 0.26 mm) for the test group and 0.43 (SD 0.22 mm) for the control group. No statistically significant differences between both groups were found. Conclusions: Within the limits of this study, implants with peri-implant defects treated with guided bone regeneration exhibited similar survival and success rates and peri-implant marginal bone loss to implants without those defects. Large-scale randomized controlled studies with longer follow-ups involving the assessment of esthetic parameters and hard and soft peri-implant tissue stability are needed