We conducted this study to investigate whether CAG repeat length in androgen receptor gene and GSTM1 and GSTT1 polymorphisms influence prostate cancer risk in Iranian newly diagnosed cancer patients compared to age-matched BPH group and healthy individuals. DNA from 110 pathologically-confirmed prostate cancer patients, 99 age-matched men with Benign Prostatic Hyperplasia (BPH) and 100 healthy individuals were extracted and amplified by polymerase chain reaction (PCR). PCR products were examined by electrophoresis and sequencing. The mean number of CAG repeat in prostate cancer patients was significantly smaller than normal (19.9 vs 22.8; p < 0.0001) and BPH groups (19.9 vs 21.9; P < 0.0001) The mean difference between normal individuals and BPH group was also significant (21.9 vs. 22.8; P = 0.003). Presence of GSTM1 null genotype were significantly higher in cancer and BPH group vs. normal individuals (both P values < 0.0001). there was not seen association between GSTT1 null or positive genotype with cancer risk, but analysis of GSTM1 null and GSTT1 positive in combination was statistically associated with Prostate cancer risk (OR = 8.4, 95% CI 1.53-46.73). Our results showed that CAG repeat polymorphism in AR gene may act as a risk modifier and GSTM1 null genotypes also may be contributed to prostate cancer susceptibility in Iranian patients.