Vitamin D receptor (VDR) is expressed in the hair follicle and the lack of it leads to alopecia. In this study, we investigated whether there was a relationship between VDR FokI gene polymorphism and alopecia areata (AA). This is the first study investigating the relationship between VDR gene polymorphism and AA. Twenty-five patients with the extensive forms of AA (alopecia totalis; AT, alopecia universalis; AU and AT/AU) and 27 healthy control subjects were genotyped. Their genotypes were determined by a polymerase chain reaction (PCR) and restriction fragment length polymorphism analysis. The genotypes were classified as FF (absence of the FokI site) and ff (presence of the FokI site). Allele frequencies for F and f alleles were 76.0% and 24.0% in the alopecic group and 72.2% and 27.7% in the control group (p > 0.05). The frequencies for the FF, Ff and ff genotypes were 56.0%, 40.0% and 4.0% in the patient group, and 48.1%, 48.1% and 3.7% in the control group, respectively. No statistically significant differences were observed in the frequencies of the VDR FokI genotype between the patient and the control groups. However, to conclude that there is no relationship between VDR gene polymorphism and AA, the VDR FokI polymorphism should be further studied in other populations, larger groups, and the distribution of other VDR polymorphisms such as BsmI, Tru9I, ApaI, TaqI and polyA.