The chromosomal translocation t(15;17)(q22:21) of acute promyelocytic leukemia (APL) fuses PML, a novel gene, with RAR alpha, a retinoic acid receptor gene. PML-RAR hybrid transcripts were studied in 18 cases of APL using RNA-PCR. Two forms were noted: one designated 5′, producing a 439-bp chimeric fragment, and a 3′ form, producing a pair of fragments of 765 bp and 909 bp. 5′ forms were found in 7 of the 18 cases while the other 11 patients expressed the 3′ forms. The chromosome 15 specific probes K3 and K2 were used to study genomic breakpoints in 12 APL patients. Comparison of these results with RNA PCR in 11 patients for whom both were available yielded a rearrangement pattern predictive of whether the hybrid transcript was 5′ or 3′. In this way, an additional three patients in whom DNA but not RNA was available were identified as having 3′ (downstream) breakpoints and, therefore, 3′ hybrid forms. Thus, 21 cases categorized as having 5′ or 3′ PML-RAR transcripts were analyzed for various phenotypic differences. Surface phenotyping of leukemic promyelocytes demonstrated expression of the CD2 antigen in all cases with the 5′ splice variant. Only 1 of 11 cases with the 3′ form showed CD2 expression. This difference is significant at P = .001.