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Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal malignancy that has the worst 5-year survival rate of all of the common malignant tumors. Surgery, chemotherapy, and/or chemoradiation remain the main tactics for PDAC treatment. The efficacy of chemotherapy is often compromised because of the substantial risk of severe toxicities. In our study, we focused on identification of polymorphisms in the genes involved in drug metabolism, DNA repair and replication that are associated with inter-individual differences in drug-induced toxicities. Using the microarray, we genotyped 12 polymorphisms in the <i>DPYD</i>, <i>XPC</i>, <i>GSTP1</i>, <i>MTHFR</i>, <i>ERCC1</i>, <i>UGT1A1</i>, and <i>TYMS</i> genes in 78 PDAC patients treated with FOLFIRINOX. It was found that the <i>TYMS</i> rs11280056 polymorphism (6 bp-deletion in <i>TYMS</i> 3′-UTR) predicted grade 1–2 neurotoxicity (<i>p</i> = 0.0072 and <i>p</i> = 0.0019, according to co-dominant (CDM) and recessive model (RM), respectively). It is the first report on the association between <i>TYMS</i> rs11280056 and peripheral neuropathy. We also found that PDAC patients carrying the <i>GSTP1</i> rs1695 GG genotype had a decreased risk for grade 3–4 hematological toxicity as compared to those with the AA or AG genotypes (<i>p</i> = 0.032 and <i>p</i> = 0.014, CDM and RM, respectively). Due to relatively high <i>p</i>-values, we consider that the impact of <i>GSTP1</i> rs1695 requires further investigation in a larger sample size.