© 2023 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.Background and Objectives: Recently, the terms autophagy and apoptosis have been studied on implants, especially in cell culture and in vitro studies, but in vivo evaluations are limited. The aim of this study was to compare the differences in apoptosis and autophagy intensity at the molecular and cellular level in periodontal and peri-implant diseases. Methods: Sixty-four biopsy samples were obtained from 52 patients, 36 female and 16 male, whose mean age was between 18 and 75, and were included in the study. The periodontitis group was defined as PG (n:30 sample) and the peri-implantitis group as IG (n:34 samples). Granulation tissues as biopsy materials were collected, and immunohistochemical analysis was performed with hematoxylin–eosin, Masson's trichrome, anti-MAP1LC3A, anti-beclin, and anti-active caspase-3 antibodies and terminal TdT-mediated dUTP-biotin nick end labeling (TUNEL) methods. The histological slide images were evaluated with the ImageJ software program. Inflammatory cell density in epithelial tissue, inflammatory cell density in connective tissue, the density of necrotic tissue debris, and collagen density in connective tissue were scored between 0 and 3 (0: none, 1: minimal, 2: moderate, 3: severe by hematoxylin–eosin and Masson's trichrome). The antibody binding reaction areas were evaluated per unit area (mm2) in connective tissue by immunohistochemical examination. Results: As histochemical evaluations, there was no statistically significant differences the mean inflammatory cell density value in the epithelial tissue, inflammatory cell density value in the connective tissue, density value of necrotic tissue debris, collagen density value in the connective tissue between the groups. There was no statistically significant difference on immunohistochemical staining with LC3, caspase-3, Beclin-1 and TUNEL between the two groups (p >.05). Conclusions: A higher rate of inflammatory accumulation was shown on peri-implantitis, but no difference was found between periodontitis and peri-implantitis according to autophagy and apoptosis markers. Studies with high sample sizes with different markers are needed.