Objectives To assess if (I) the alveolar bone defect configuration at dental implants diagnosed with peri-implantitis is related to clinical parameters at the time of surgical intervention and if (II) the outcome of surgical intervention of peri-implantitis is dependent on defect configuration at the time of treatment. Materials and methods In a prospective study, 45 individuals and 74 dental implants with >= 2 bone wall defects were treated with either an autogenous bone transplant or an exogenous bone augmentation material. Defect fill was assessed at 1 year. Results At baseline, no significant study group differences were identified. Most study implants (70.7%,n= 53) had been placed in the maxilla. Few implants were placed in molar regions. The mesial and distal crestal width at surgery was greater at 4-wall defects than at 2-wall defects (p= 0.001). Probing depths were also greater at 4-wall defects than at 2-wall defects (p= 0.01). Defect fill was correlated to initial defect depth (p< 0.001). Defect fill at 4-wall defects was significant (p< 0.05). Conclusions (I) The buccal-lingual width of the alveolar bone crest was explanatory to defect configuration, (II) 4-wall defects demonstrated more defect fill, and (III) deeper defects resulted in more defect fill.