No consecutive analysis of BAALC and WT1 expressions associated with core‐binding factor AML (CBF‐AML) from diagnosis to hematopoietic stem cell transplantation (HSCT) has yet been reported. We investigated BAALC and WT1 expressions using a method of real‐time quantitative polymerase chain reaction (RQ‐PCR) at diagnosis, after induction chemotherapy, at pre‐HSCT, and at post‐HSCT period in 45 consecutive patients [t(8,21) (n = 28), inv(16) (n = 17)], who received HSCT as a post‐remission treatment. BAALC and WT1 RQ‐PCR decrement ratio (DR) was also calculated at post‐induction chemotherapy, at pre‐HSCT, and at post‐HSCT compared with the diagnostic level. Higher BAALC expression at diagnosis showed significantly inferior OS (P = 0.031), EFS (P = 0.011), and higher CIR (P = 0.002) rates. At post‐HSCT, both higher BAALC and WT1 expressions showed significantly inferior OS (P = 0.005, 0.016), EFS (P = 0.002, 0.006), and higher CIR (P = 0.001, 0.003) rates. A subgroup of t(8;21) showing higher BAALC and WT1 expressions at post‐HSCT were also associated with inferior OS (P = 0.018, 0.015) and higher CIR rates (P = 0.019, 0.011). While BAALCDR showed no significant results on outcomes, WT1 DR more than 2‐log at post‐HSCT showed significantly lower CIR rate (P = 0.028). This study showed that higher post‐HSCT BAALC and WT1 expressions in patients with CBF‐AML may be good markers of minimal residual disease for the prediction of survival and relapse after HSCT.