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The aim of this study was to compare the oral cavity status with the species composition of microorganisms colonizing the mouth of patients with or without systemic diseases. Seventy-seven men and women, 19 to 65-years-old, of four groups: hemodialyzed patients (HD), kidney allograft recipients (Tx), congenitally disordered (Cd) and control (C) patients (without systemic diseases) were examined clinically for the oral cavity status and the microorganisms occurring in the mouth were identified. Swabs and samples taken from dental plaques, pockets and periodontium were used for light and electron microscopical studies as well as for protozoan, bacterial and fungal cultures. Entamoeba gingivalis and Trichomonas tenax were found in the HD, Tx, Cd and C groups (top prevalence 14, 14, 87.5 and 25%, respectively); free-living amoebae (with some features of Acanthamoeba sp.) also occurred in several cases. Staphylococcus aureus bacteria were found in 66% of Cd patients infected with the protozoans. Numerous fecal bacteria and/or fungi Candida albicans have been observed in 41-51-year-old Cd and HD patients. In all patient groups, it was the 41n51-year-olds who showed the highest prevalence of protozoans, bacteria and fungi. The results indicate that metabolic disabilities favour pathological changes in periodontal tissues and may influence the species composition of mixed protozoan, bacterial and/or fungal infections in various ways, in patients with different systemic diseases.