The experiment was conducted on 30 Holstein-Friesian cows: 10 cows in the follicular phase of the cycle and in the luteal phase 10 d later, 10 cows with follicular cysts, and 10 with luteal cysts. The presence of the ovarian structures was confirmed by ultrasonography. Serum levels of progesterone and 17β-oestradiol were tested with ELISA. Samples for cytological examination were collected from the uterus of all cows using a cytological brush. Following staining, the smears were evaluated in terms of quality and percentages of endometrial cells. In the follicular phase of the oestrous cycle, cells of type A -superficial cells (64.6 ± 4.48) were proportionally the largest group of cells. Cells of type C -basal cells (19.8 ± 2.75) were also present. In the luteal phase, the highest percentage of cells was of type B -intermediate cells (76.9 ± 4.26). When follicular cysts were present on the ovaries, the cytology resembled the follicular phase of the cycle, but with many younger type C cells (33.1 ± 4.11). In the case of luteal cysts on the ovaries, the cytology was similar to that of the luteal phase of the cycle, however with a lower percentage of type B cells (58.1 ± 5.71), and a slightly higher percentage of the other types. The differences in the cytological image of the uterus when different ovarian structures are present, depend on the hormonal activity of those structures. Due to the lack of literature data, the results of the study are important as a model, and may substantially facilitate identification of phases of the oestrus cycle, or the pathologies described, as well as indicate the current status of the endometrium.