Peri-implantitis is a condition that includes soft tissue inflammation and rapid loss of bone. Treatment of peri-implantitis includes both antimicrobial and bone augmenting methods. The question of whether true re-osseointegration may occur following treatment of peri-implantitis is controversial. The aim of this study was to investigate whether the character of the implant surface was of importance for the occurrence of re-osseointegration following treatment of peri-implantitis. Four beagle dogs were used. The mandibular premolars were extracted. After 12 months, 3 ITI(R) solid screw dental implants were placed in each side of the mandible. In the left side, implants with a turned surface (Turned sites) were used, while in the right side implants with a SLA surface (SLA sites) were placed. After 3 months of healing, peri-implantitis was induced by ligature placement and plaque accumulation. When about 50% of the initial bone support was lost, the ligatures were removed. Five weeks later, treatment was initiated. Each animal received tablets of Amoxicillin and Metronidazole for a period of 17 days. Three days after the start of the antibiotic regimen, one implant site (experimental site) in each quadrant was exposed to local therapy. Following flap elevation, the exposed titanium surface was cleaned with the use of cotton pellets soaked in saline. The implants were submerged. Six months later, biopsies were obtained. Treatment resulted in a 72% bone fill of the bone defects at Turned sites and 76% at SLA sites. The amount of re-osseointegration was 22% at Turned sites and 84% at SLA sites. A treatment regimen that included (i) systemic administration of antibiotics combined with (ii) granulation tissue removal and implant surface cleaning resulted in resolution of peri-implantitis and bone fill in adjacent bone defects. Further, while substantial "re-osseointegration" occurred to an implant with a rough surface (SLA), bone growth on a previously exposed smooth surface (Turned) was minimal.