Abstract Second primary tumors (SPTs) and local-regional recurrence negatively impact the prognosis of patients with curatively treated early-stage head and neck cancer. Genetic variations in microRNA (miRNA) biogenesis genes have been found to be associated with the risk of multiple solid tumors. Thus, we hypothesized that these variations were also associated with the risk of SPT/recurrence in patients with early-stage head and neck cancer. We performed a nested case-control study including 150 early-stage head and neck cancer patients with SPT/recurrence and 300 patients without SPT/recurrence. We genotyped 71 tagging and potentially functional single nucleotide polymorphisms (SNPs) from eight miRNA biogenesis pathway genes (RNASEN, DGCR8, DICER1, EIF2C1, DDX20, GEMIN4, RAN, XPO5). Seven SNPs in RNASEN, one in XPO5, and one in RAN were significantly associated with the risk of SPT/recurrence. The most significant SNP was rs7735863, an intronic SNP in RANSEN. The variant-containing genotypes of this SNP were associated with a 1.72-fold increased risk (95% confidence interval [CI], 1.16–2.57; P=0.0076). A combined analysis showed that compared with the patients without any unfavorable genotypes, the SPT/recurrence risk was increased 1.50- (95% CI, 1.02–2.22) and 2.69-fold (95% CI, 1.59–4.53) for those with one and two unfavorable genotypes, respectively (P for trend<0.001). Survival tree analysis further identified potential higher-order interactions and categorized the study subjects into different risk groups. Compared to the low-risk group with an event-free median survival time (MST) over 96 months, patients in the high-risk group had a 5.02-fold increased risk (95% CI, 2.70–9.31; P=3.20×10−7) and an event-free MST of 31.4 months (log rank P=1.25 − 10−7). Our results suggest that genetic polymorphisms within the miRNA biogenesis pathway may be used individually and jointly to predict the risk of SPT/recurrence of early-stage head and neck cancer patients. Citation Information: Cancer Prev Res 2010;3(1 Suppl):PR-03.