The single-gene approaches in association studies of polygenic diseases are likely to provide limited value in predicting risk. The combined analysis of genetic variants that interact in the same pathway may amplify the effects of individual polymorphisms and enhance the predictive power. To evaluate higher order gene-gene interaction, we have examined the contribution of four angiogenic gene polymorphisms (VEGF-1154G/A; VEGF-634G/C; MMP9-1562C/T and TSP1-8831A/G) in combination to the risk of prostate cancer. For the combined analysis of VEGF and MMP9 SNPs, we found a significant gene-dosage effect for increasing numbers of potential high-risk genotypes. Compared to referent group (low-risk genotypes), individuals with one (OR = 2.79, P = 0.1), two (OR = 4.57, P = 0.02) and three high-risk genotypes (OR = 7.11, P = 0.01) had increasingly elevated risks of prostate cancer. Similarly, gene-gene interaction of VEGF and TSP1 polymorphisms increased risk of prostate cancer in additive manner (OR = 6.00, P = 0.03), although the TSP1 polymorphism itself was not associated with the risk. In addition, we examined the synergistic effect of these polymorphisms in relation to prostate cancer prognosis according to histopathological grade and clinical stage at diagnosis. Cross-classified analysis revealed potential higher order gene-gene interactions between VEGF and TSP1 polymorphisms in increasing the risk of developing an aggressive phenotype disease. Patients carrying three high-risk genotypes showed a 20-fold increased risk of high-grade tumor (OR = 20.75, P = 0.002). These results suggest that the gene-gene interaction of angiogenic gene polymorphisms' increased risk of prostate cancer onset and aggressiveness.