Aim. To identify the difference in the detection of yeasts of the genus Candida and their species composition in people with gastrointestinal pathology and in healthy people undergoing a regular medical checkup.Materials and methods. Clinical trial material comprised biological material from patients undergoing regular medical checkup (control group) and patients with intestinal pathology. Following the detection of fungal colonies on Sabouraud medium, identification was carried out using chromogenic agar. A number of strains were identified via mass spectrometry.Results. The study results show that the frequency of occurrence of the genus Candida is more than three times higher in patients with intestinal pathology. In addition, the study groups revealed the differences in the species composition. Candida krusei is more than 5 times more common in cases of gastrointestinal pathology.Conclusion. Due to the differences in the frequency and species composition of yeasts of the genus Candida isolated from the intestine, specialists should diagnose intestinal diseases and choose antimycotic therapy in a meticulous way.