Renal cell carcinoma (RCC) accounts for ∼4% of all human malignancies and is the 9th leading cause of male cancer death in the United States. The purpose of this study was to determine the effect of variation within microRNA (miRNA)-binding sites of genes in the VHL-HIF1α pathway on RCC risk. We identified 429 miRNA-binding site single-nucleotide polymorphisms (SNPs) in 102 pathway genes and assessed 53 tagging-SNPs for 31 of these genes for risk in a case–control study consisting of 894 RCC cases and 1,516 controls. Results showed that five SNPs were significantly associated with RCC risk. The most significant finding was rs743409 in MAPK1. Under the additive model, the variant was associated with a 10% risk reduction (OR: 0.90, 95% CI, 0.77–0.98). Other significant findings were for SNPs in CDCP1, TFRC, and DEC1. Cumulative effects analysis showed that subjects carrying four or five unfavorable genotypes had a 2.14-fold increase in risk (95% CI, 1.03–4.43, P = 0.04) than those with no unfavorable genotypes. Potential higher-order gene–gene interactions were identified and categorized subjects into different risk groups. The OR of the high-risk group defined by two SNPs: CDCP1:rs6773576 (GG) and DEC1:rs10982724 (GG) was 4.46 times higher than that of low-risk reference group (95% CI, 1.31–15.08). Overall, our study provides the first evidence supporting a connection between miRNA-binding site SNPs within the VHL-HIF1α pathway and RCC risk. These novel genetic risk factors might help identify individuals at high risk to enable detection of tumors at an early, curable stage. © 2013 Wiley Periodicals, Inc.