Abstract Background Research on vitamin D deficiency has recently surged in popularity. This issue has been acknowledged as a widespread problem, often called a "pandemic", and approximately 90% of the Polish population suffers from vitamin D deficiency. The 3-epi-25(OH)D2 and 3-epi-25(OH)D3 metabolites are stereoisomers of 25(OH)D2 and 25(OH)D3 metabolites, and they may be accidentally measured when determining 25(OH)D levels and result in overestimating metabolite concentrations. Purpose Our study aims to identify vitamin D hydroxy metabolites (25-hydroxyvitamin D2, 25-hydroxyvitamin D3, and their epimers 3-epi-25-hydroxyvitamin D2 and 3-epi-25-hydroxyvitamin D3) in patients with cardiovascular disease and healthy volunteers. To our knowledge, no similar studies have been conducted on this topic. Method We included 27 adult patients with venous thrombosis (fourteen males and thirteen females, aged 64.11±14.84 years) and 35 healthy volunteers (thirty-three females and two males, aged 36.37±12.29 years). We used our validated UPLC-MS/MS method to measure the concentrations of 25(OH)D2, 25(OH)D3, 3-epi-25(OH)D2, and 3-epi-25(OH)D3. Statistica 13.3 with Plus Kit 3.0 was used for the statistical assessment. Normal variables were represented as mean and standard deviation, and non-normal variables as the median and interquartile range. A P-value < 0.05 was considered statistically significant for all tests. Results Patients had significantly lower levels of epi-25(OH)D2 than the healthy control group (0.6 [0.4] ng/mL vs. 2.2 [1.3-4.3] ng/mL, p = 0.004). Similarly, they exhibited significantly lower levels of %epi-25(OH)D2 (8.6 [6-22.3] % vs. 39.4 [18.5] %, p = 0.035). Females had higher levels of 25(OH)D3 than males (26.5 [16.2-37.9] ng/mL vs. 18.8 [7.5] ng/mL, p = 0.04). They also exhibited higher levels of total 25(OH)D3 (30.3 [15.6] ng/mL vs. 19.4 [7.8] ng/mL, p = 0.016). Higher age (OR 1.12, 95% CI 1.07 to 1.18), being male (OR 17.77, 95% CI 3.54 to 89.3), and lower % 3-epi-25(OH)D2 (OR 0.92, 95% CI 0.84 to 0.998) were univariate predictors for patients with venous thrombosis. Conclusion: Demographic factors within a given population may affect the 25(OH)D3 concentration. The results indicate that vitamin D epimeric metabolites, particularly epi-25(OH)D2, and their percentage were different in patients compared to healthy volunteers. Additional studies involving a larger population are necessary to fully comprehend the relationship between these vitamin D epimeric metabolites and cardiovascular health