Chemokines and their receptors may contribute to pathologic processes such as cell proliferation, angiogenesis, invasion and metastasis of different types of cancers. In the present study, we aimed to investigate the association between SDF1-3A’ and CXCR4 gene polymorphisms and the susceptibility and clinicopathological development of prostate cancer. Consecutive patients with histologically confirmed prostate cancer (n= 152) and healthy controls (n= 149) with normal serum total PSA (< 4 ng/ml) and DRE were prospectively enrolled in this study between 2007 and 2011. SDF1-3’A and CXCR4 gene polymorphisms were assessed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) in all subjects. For the statistical analyses Pearsons’s Chi-Squared (χ2) , Mann-Whitney U and multiple logistic regression model tests were used where appropriate. The mean age and smoking status were similar in prostate cancer patients and controls. Total PSA levels were significantly increased in the prostate cancer patients compared with controls. There were no significant differences in the distributions of SDF-1 and CXCR4 genotypes between controls and prostate cancer patients. However, the patients with prostate cancer with AA genotype of SDF1-3’A gene had an increasing risk of 2.02 fold (aOR= 2.02; 95% CI= 1.05-3.90; p= 0.035) to develop high pathological T stage when compared with prostate cancer patients with GG homozygotes of SDF1-3’A gene after being adjusted for age, BMI and smoking status. In addition, the distribution of AA genotype of SDF1-3’A gene polymorphism was found significantly increased in the patients with bone metastasis in comparison to those without bone metastasis (aOR=2.94; 95% CI=1.26-6.82; p=0.012). On the other hand, CXCR4 gene polymorphism was not associated with the clinicopathological characteristics of prostate cancer. Our results suggest that SDF1-3’A gene polymorphism may be associated with the progression and bone metastasis of prostate cancer.