Multiple primary tumors (MPT), especially in the hypopharynx and esophagus, are challenging in patients with head and neck cancer (HNC). Alcohol and alcohol-metabolizing genes were reported to be related to upper digestive tract cancers. Here, we investigated whether the genotypes of alcoholmetabolizing enzymes (ADH1B, ADH1C, and ALDH2) affected patients' susceptibility to developing MPTs. We recruited 659 male patients with HNC between March 1996 and February 2017. Age-and gender-matched controls were also recruited. A total of 164 patients with HNC were identified to have second or third malignancies. The single-nucleotide polymorphisms in ADH1B (rs1229984), ADH1C (rs698), and ALDH2 (rs671) were analyzed by Taq-Man assays. The prevalence of ALDH2 à 2 allele carriers is significantly higher than that of à 1 à 1 homo-zygotes for oral cavity (P ¼ 0.013) and oropharyngeal cancers (P ¼ 0.012). For ADH1B, the number of à 1 allele carriers is significantly higher than that of à 2 à 2 homozygotes for oropharyngeal (P ¼ 0.017) and hypopharyngeal cancers (P < 0.001). ADH1C (rs698) SNPs are not significantly associated with tumor subsites (all P > 0.05). Polymorphisms in ALDH2 (à 2 allele carriers) and ADH1B (à 1 allele carriers) significantly increase the risk of developing MPTs in the upper digestive tract [P < 0.001, OR (95% confidence interval (CI): 5.186 (2.444-11.004) and P < 0.05, OR (95% CI): 2.093 (1.149-3.812), respectively]. ALDH2 (rs671) à 2 and ADH1B (rs1229984) à 1 allele carriers were shown to develop MPTs in the upper digestive tract. Genetic information may be used to identify high-risk patients for the development of MPTs.