Objective: The aim was to investigate the presence of Entamoeba gingivalis and Trichomonas tenax in peri-implantitis lesions. Method and materials: A total of 141 individuals were included in this study, of which 40 had clinically healthy implants (group H); the remaining were associated with peri-implantitis (group P). Gingival crevicular fluid was collected using absorbent paper, followed by a dental plaque sample from the peri-implant sulcus/pocket using a titanium curette. The samples were transferred into an Eppendorf tube. Each specimen was divided into two parts. One part was examined under a light microscope at a 10 × and 40 × magnification to detect parasites. The other part was spread on a microscope slide, stained with Giemsa stain, and examined under a microscope at 100 × magnification. Pearson chi-square test was used in the statistical analysis of data, with a significance level of P .05. Results: Although there was no presence of parasite around the healthy implants, two parasites were detected in peri-implantitis lesions. Out of 101 lesions, 31 (30.7%) showed E gingivalis, and 34 (33.6%) presented with T tenax. There was a statistically significant difference between the presence of E gingivalis and demographic data including gender, education status, frequency of dental visits, and brushing frequency. Presence of T tenax in lesions was correlated with frequency of dental visits (P .05). It was observed that E gingivalis and T tenax were mostly detected in the mandible (P = .004 and .014, respectively) in comparison with the maxilla. Conclusion: This study showed that peri-implantitis lesions were involved with E gingivalis and T tenax, in contrast to the healthy areas. Keywords: dental implants, direct microscopy, Giemsa staining, microbiology, parasite, peri-implantitis