Objective　To investigate the association between single nucleotide polymorphisms (SNP) (rs116855232 in NDUT15 gene) and acute lymphocytic leukemia (ALL) in Chinese Han children. Methods　A total of 133 children with ALL were recruited in this study, and were divided into two groups based on white blood cell count (WBC) as of WBC≤2.0×109 group and WBC＞2.0×109 group. Genotypes of each patient were detected using PCR-RFLP. WBC, initial and average dose of 6-mercaptopurine (6-MP) were collected. Results　In this study, we found 4 patients with TT genotype, 31 patients with CT genotype and 98 patients with CC genotype; and there is a difference in genotypes between the two groups in initial stage (P=0.007) and in maintenance therapy stage (P=0.005). In maintenance therapy stage, patients with TT genotype received a lower dose of 6-MP than that for patients with other genotypes (P<0.01). Conclusions　The polymorphism of rs116855232 in NDUT15 gene was associated with leucopenia induced by 6-mercaptopurine in children with ALL, and patients with TT genotype were suggested to use a lower dose of 6-MP to avoided serious leucopenia.