In this study, we report three cases of novel KMT2A partner genes uncovered as a result of comprehensive cytogenetic and molecular genetic approach—Bruton’s tyrosine kinase (BTK) in infant AML with (X;11)(q22.1;q23.3), NUT family member 2A (NUTM2A) in pediatric secondary T-cell ALL with t(10;11)(q22;q23.3), and pre-mRNA processing factor 19 (PRPF19) in infant AML with inv(11)(q12.2q23.3). Here, NUTM2A is linked to acute myeloid leukemia.