Background: The contribution of genetic factors in hypertension cannot be denied. Methods: In this study we evaluated the relationship between vitamin D receptor (VDR) gene polymorphisms ( Bsm-I, Apa-I and Fok-I), and target organ damage in 74 patients (female/male 49/25, mean age 49.2 ± 8 years) with essential hypertension. The VDR genotypes were evaluated by polymerase chain reaction and digestion of the amplified products by related enzymes. Patients with diabetes mellitus or impaired glucose tolerance and severe obesity were excluded. All patients underwent a complete physical examination, full biochemistry and urinalysis; in addition, all of them were assessed for target organ damage. Twenty-four-hour ambulatory blood pressure monitoring was performed in all patients. Results: No significant difference was detected in biochemistry results and physical examination between groups for Bsm-I and Apa-I VDR gene polymorphisms. Patients were distributed as FF (n = 39) and non-FF (Ff/ff, n = 35) for Fok-I polymorphism. A negative correlation was present between vitamin D levels and day-time interval and early morning average by the measurement of 24-hour ambulatory blood pressure in the non-FF group. Serum cystatin-C was higher in the non-FF group (p = 0.012). In addition on retinal examination, the degree and presence of retinopathy were significantly higher in the non-FF group when compared to the FF group (p = 0.025, p = 0.018, respectively). Conclusion: Knowing the VDR gene polymorphisms status may be helpful in preventing target organ damage in hypertensive patients.