Congenital leukemia is a rare event with a poor prognosis. We report a case of congenital leukemia with a cryptic rearrangement of MLL demonstrable only with RT-PCR. Interestingly, with treatment, the patient showed lineage plasticity of the leukemia with the development of monocytic lineage blasts after presenting with B-cell lineage blasts. This was heralded by the development of a new clonal cytogenetic abnormality. This case highlights the primitive nature of the leukemic cells in congenital leukemia, and emphasizes that RT-PCR for MLL rearrangements may identify a subset of cases which are otherwise negative by karyotyping, FISH, and chromosomal microarrays.