Molecular techniques to detect MLL (11q23) and AF-4 (4q21) gene rearrangements are being evaluated for use in stratification of patients into prognostic groups. We studied 15 cases of infant acute lymphoblastic leukemia (ALL) with Southern blotting for MLL gene rearrangement and reverse transcriptase-polymerase chain reaction (RT- PCR) for t(4;11) fusion transcripts and compared the results to cytogenetic and clinical data. Our results indicate that classic t(4;11)(q21;q23) translocations are detected by RT-PCR; however, unusual 4;11 translocations still require additional investigation. We also extended and updated our original study of MLL gene rearrangement in infant ALL to 40 patients with longer follow-up and show that the group with germline configuration of the MLL gene continues to have an excellent outcome. The results of salvage therapy (bone marrow transplantation or chemotherapy) suggest that transplant may show advantage. Preliminary results of the use of RT-PCR to assess minimal disease are also reported.