In this study investigating the genomic landscape of CRLF2‐r ALL, we have confirmed the high incidence of CRLF2‐r in DS‐ALL, demonstrated its co‐existence with other primary chromosomal rearrangements and enrichment of specific chromosomal gains and deletions of IKZF1, BTG1, ADD3, SERP2, TSC22D1, SLX4IP, and PBX3. There were significant differences in CNA profiles between P2RY8‐CRLF2 and IGH‐CRLF2 patients with an increased incidence of IKZF1, BTG1, and ADD3 deletions and a higher age at diagnosis being observed in the latter. Here, IKZF1 is linked to acute lymphoblastic leukemia.