Abstract: OBJECTIVE To establish an accurate, rapid and economical method for detecting NUDT15 c.415C>T and TPMT*3C gene polymorphisms and evaluate the value of their clinical application. METHODS Serum samples of patients taking azathioprine for more than 2 weeks from May 2017 to May 2018 in Fujian were collected. NUDT15 c.415C>T and TPMT*3C were genotyping by PCR-restriction fragment length polymorphism (PCR-RFLP), PCR-Sanger, and real-time PCR. The accuracy, simplicity and economy of the three methods were compared. The association between genetic polymorphisms and azathioprine-induced leukocyte reduction was analyzed in combination with clinical data. RESULTS A total of 129 patients were included, 15 (11.6%) of whom developed leukopenia. The results of the methods were essentially equivalent. No mutant homozygote genotype was found in TPMT*3C gene. There was strong associations of NUDT15 c.415C>T with azathioprine-induced leukopenia (OR=6.2, 95%CI:2.5~15.4, P=0.000 054), whereas there was no relevance for TPMT*3C (P=0.393). The predictive sensitivity of NUDT15 c.415C>T was 53.3%,specificity was 85.1%, and AUC of ROC curve was 0.69. CONCLUSION The three methods can be used for clinical detection of NUDT15 c.415C>T and TPMT*3C gene polymorphisms. The PCR-RFLP method does not require special kit, no expensive equipment, low cost, simple process, easy operability, and especially applicable to the basic medical institutions or scientific research units with limited conditions. The detection of NUDT15c.415C>T gene polymorphisms for Fujian Han patients with azathioprine has better clinical value than the detection of TMPT*3C.