In addition to the major fusion gene PML-RAR alpha, the t(15; 17) in acute promyelocytic leukemia (APL) produces the reciprocal fusion gene RAR alpha-PML. To determine the scope of RAR alpha-containing mRNA expression in APL cells, we tested PML-RAR alpha-positive APL cells for the presence of mRNAs initiated from two distinct RAR alpha gene promoters, alpha1 and alpha2. From the normal allele, both RAR alpha1 and RAR alpha2 mRNAs were expressed in all APL cases (N = 24). From the translocated allele, RAR alpha1-PML mRNA was expressed in 77% and RAR alpha2-PML mRNA in 28% of cases (N = 98). RAR alpha2-PML mRNA was not observed in the absence of RAR alpha1-PML mRNA. There was no association between RAR alpha1-PML or RAR alpha2-PML mRNA expression and the type of PML-RAR alpha mRNA formed by either 5' or 3' breaksites in the PML gene. RAR alpha1-PML mRNAs and RAR alpha2-PML mRNAs from 5' PML breaksite cases coded for full-length RAR alpha-PML proteins but RAR alpha2-PML mRNAs from 3' PML breaksite cases encoded a truncated RAR alpha2 peptide. RAR alpha1/alpha2-PML mRNA expression was not associated with differences in APL cell sensitivity to all-trans retinoic acid(tRA)-induced differentiation in vitro or in clinical outcome after tRA or chemotherapy induction therapy (protocol E2491). Our analysis indicated that RAR alpha1/alpha2-PML mRNA expression markedly differs from normal RAR alpha1/alpha2 mRNA expression, that the difference in RAR alpha1-PML and RAR alpha2-PML mRNA expression frequency is primarily related to the genomic separation of the RAR alpha1 and RAR alpha2 coding exons, and that variations in RAR alpha1/alpha2-PML mRNA expression likely have no clinically relevant function in APL cells.