Colonization of the oral cavity with microorganisms begins in infancy. Besides numerous bacteria and fungi that inhabit the oral cavity, protozoa can also be found there. Entamoeba gingivalis and Trichomonas tenax are eukaryotic microorganisms that inhabit various places in the oral cavity, including the periodontal space. These unicellular organisms are similar to other protozoa based on various factors including morphology and life cycle. Although the epidemiological data differs, the prevalence of E.gingivalis is higher compared to T.tenax, and the abundance in the oral cavity depends on the inflammatory state of periodontium. The correlation between protozoan infection and periodontitis according to the data, of thus far insufficiently conducted research, suggest there is a role in the pathophysiology of inflammation of the teeth supporting tissues. The possibility of damaging the cells of oral tissues is realized by the synergy of different virulence factors. Discovered abilities of adhesion, ingestion of human cells, invasion into gingival epithelium and stimulation that leads to activation of pro-inflammatory cytokines explain the connection with the inflammatory state of periodontium. Nowadays, diagnostics of protozoa includes culturing in different media and microscopy, and molecular and immunological methods that have higher sensitivity. In addition to periodontitis, oral protozoa can be linked to other diseases such as peri-implantitis, caries and pulmonary trichomoniasis. The therapy of these infections is carried out together with the therapy of periodontitis. It includes meticulous oral hygiene which mechanically removes deposits, usage of additional agents with active ingredients, non-surgical periodontal therapy and, potentially, antimicrobial treatment.