Background/objective B-cell acute lymphoblastic leukemia (B-ALL) is the most common acute leukemia in children. There are many overlaps between leukemic lymphoblast and hematogones regarding their morphologic and immunophenotypic characteristics. CD123 is one of the markers that can be used to distinguish between leukemic lymphoblast and hematogones. In this study, we aimed to demonstrate the pattern of CD34/CD123 expression in hematogones and leukemic lymphoblast to monitor therapy response and detect minimal residual disease. Patients and methods This case–control study was conducted on 40 newly diagnosed patients with B-lineage ALL. They were 14 boys and 26 girls with a mean age of 4.29±2.31 and a range from 2 to 10 years. Expression of CD34/CD123 by flow cytometry was carried out at diagnosis and at the end of induction. In addition, 20 patients with reactive bone marrow were included to asses hematogones. Results In the patient group, cells with dim CD45 were found in 24 cases, 75% of them expressed CD34 and 83.3% expressed CD123. In addition, cells with moderate CD45 were 16, all expressed CD34 and 87.5% of them expressed CD123. Thirty-two (80%) leukemic blasts expressed both CD34 and CD123; in contrast, in four (10%) patients neither antigen was expressed. In hematogones, immature hematogones (dim CD45, CD34+) did not express CD123, whereas 75% of mature hematogones (moderate CD45, CD34−) expressed CD123. On the other hand, at the end of induction, 18 (45%) leukemic blasts expressed both CD34 and CD123 and four (10%) showed no expression of both antigens. Conclusion This distinct pattern of CD34 and CD123 expression on B-ALL blasts (concordant) and hematogones (discordant) can help differentiate residual leukemic blasts from hematogones in patients with B-ALL.