The aim of this study is to measure the frequencies of the most common variants involved in 6-MP metabolism—TPMT*3C (rs1142345), NUDT15 c.415C>T (rs116855232), and ITPA c.94C>A (rs1127354)—in children with ALL from Yunnan province and to indicate whether these genetic variants could predict 6-MP toxicity and tolerable dose during ALL maintenance therapy. Here, ITPA is linked to acute lymphoblastic leukemia.