Background Thiopurine methyltransferase (TPMT) polymorphism is one of the causes of the toxicity of thiopurines, but this is rarely seen in Asian populations. Rather, the nucleoside diphosphate‐linked X‐component motif 15 (NUDT15) gene is frequently linked to mercaptopurine (MP) intolerance and myelotoxicity in children with acute lymphoblastic leukemia (ALL) in East Asians; however, little is known about the NUDT15 polymorphism in healthy children, especially in ethnic minorities in China. Methods A total of 162 cases of healthy children with Bai nationality were enrolled for NUDT15 genotyping. Results Three coding variants were identified in the NUDT15 gene including rs186364861, rs746071566 and rs116855232. Notably, the rs746071566 and rs116855232 in NUDT15 showed much higher frequencies in healthy children with Bai nationality compared with healthy East Asian populations, suggesting a concentrated distribution of these variants in the Bai ethnic group. Conclusions This finding reveals the genetic polymorphism of NUDT15 in children with Chinese Bai nationality, providing a biological genetic background for the individualized therapy of thiopurines for children with Bai nationality in China.