Intervertebral disk degeneration(IDD) is strongly associated with genetic predisposition and environmental susceptibility. Several studies been conducted to investigate the potential association between IDD and Fok I polymorphism located in the gene encoding the vitamin D receptor(VDR), and inconsistent conclusions had been reached among different ethnic populations. In order to assess the association between the Fok I polymorphism and the risk of IDD, we performed a comprehensive and systematic meta-analysis. Candidate articles were retrieved from Pub Med,EMBASE, China National Knowledge Infrastructure(CNKI), and China Biology Medical(CBM) with strict inclusion criteria in January 2015. Among the 54 articles that were retrieved, only eight studies met the inclusion criteria. The pooled data analysis based on allele contrast, homozygote, heterozygote, dominant, and recessive models revealed no significant correlation between the Fok I polymorphism and the risk of IDD. However, when stratified by ethnicity, significant associations were detected for Hispanics based on allele contrast(OR = 1.395, 95% CI = 1.059–1.836,P = 0.018), homozygote(OR = 1.849, 95% CI = 1.001–3.416, P = 0.049), heterozygote(OR = 1.254, 95% CI = 1.049–1.498, P = 0.013), and dominant(OR = 1.742, 95%CI = 1.174–2.583, P = 0.006) models, and for Asians using the dominant model(OR = 1.293,95% CI = 1.025–1.632, P = 0.030), whereas there is no significant association detected for Caucasians. In conclusion, Fok I polymorphism is not generally associated with IDD, but there is increased risk for IDD in Hispanics and Asians carrying Fok I allele T.