Objectives: to evaluate and compare clinical presentations, medical history, and laboratory data of patients with polycystic ovary syndrome, including vitamin 25(OH)D3 level. Methods: In total, 81 patients were examined. The patient group included 51 patients with signs of polycystic ovary syndrome. The control group included 30 healthy women without signs of polycystic ovary syndrome, comparable according to gender and age to the patient group. Polycystic ovary syndrome was verified based on the diagnostic Rotterdam and international polycystic ovary syndrome guidelines’ criteria. The levels of cholecalciferol were determined by mass spectrometry (ng/mL). At the second stage of the study, the patient group with polycystic ovary syndrome was divided into two subgroups depending on the waist circumference and compared with each other by the level of insulin, low-density lipoproteins, triglycerides, anti-Mullerian hormone, follicle-stimulating hormone, and luteinizing hormone. Statistical analysis was carried out using the parametric t-test for two-independent samples with equal or different variance. For nominal data—Pearson’s chi-test, when the means are not calculated and a test is carried out for the presence of a relationship between the nominal variables. Results: Patients with polycystic ovary syndrome and without polycystic ovary syndrome did not have a statistically significant difference in 25(OH)D3 level. Statistically significant differences in the level of 25(OH)D3 were found in women with polycystic ovary syndrome with the waist circumference ⩾80 cm. In these subgroups, differences in insulin, low-density lipoprotein, and triglycerides levels were also revealed. Conclusion: The correlation of the 25(OH)D3 level does not differ in the groups of patients with polycystic ovary syndrome and without polycystic ovary syndrome, but significantly correlates with the metabolic profile of patients. © The Author(s) 2020.