Objective <p>The aim of the study was to evaluate the association between <i>T. tenax</i> and <i>E. gingivalis</i> with peri-implant and periodontal diseases compared to healthy controls.</p> Material and Methods <p>A total of 140 participants were included in four groups in this study. The groups included 35 patients with peri-implantitis and periodontitis (IP+P group); 35 patients with peri-implant and periodontal health (IH+PH group); 35 patients with periodontitis (P group), and 35 periodontally healthy individuals (PH group). Clinical periodontal and peri-implantitis parameters were recorded. Plaque samples were taken from around teeth in P and PH groups and around implants and teeth in IP+P and IH+PH groups. The presence of <i>T. tenax</i>and<i>E. gingivalis</i> was determined under a microscope.</p> Results <p>The detection of <i>T. tenax</i> and <i>E. gingivalis</i> parasites in tooth samples was higher in the IP+P and P groups than in the IH+PH and PH groups (<i>p</i>&lt;0.001). Both parasites were detected more frequently in peri-implant samples in the IP+P group than in the IH+PH group (<i>p</i>&lt;0.001 and <i>p</i>=0.001, respectively). There was no difference in parasite detection between tooth and peri-implant samples in the same host in the IP+P and IH+PH groups (p³0.05). The presence of <i>T. tenax</i> and<i>E. gingivalis </i>was associated with the presence of periodontal disease, and severity and grading of periodontitis independently of other factors (<i>p</i>&lt;0.05).</p> Conclusion <p>The presence of <i>T. tenax</i> and <i>E. gingivalis</i> might be associated with peri-implantitis and periodontitis lesions. The detection of parasites is similar on tooth and implant surfaces in the same mouth.</p> Clinical Relevance <p>Protozoa found at sites of disease may not imply a direct causal relationship with the disease; nevertheless, their detection can indicate opportunistic microbial activity or ongoing oral inflammation.</p>