A brain-enriched protein tyrosine phosphatase termed STEP46 (striatal enriched phosphatase) was previously isolated and characterized. Immunological studies with a STEP monoclonal antibody recognized several STEP-immunoreactive proteins, and suggested that additional STEP-related polypeptides existed. This study reports the isolation of two alternatively spliced transcripts of the STEP gene. One of these, STEP20 (with a predicted molecular mass of 20 kDa) was further characterized and found to lack the conserved tyrosine phosphatase domain. Northern analysis detected a 2.8 kb STEP20 message in mouse brain. The second alternatively spliced transcript, STEP61, has a 5'-extended open reading frame that encodes a protein with a predicted molecular mass of 61 kDa and contains a single tyrosine phosphatase domain. The exon-intron organization responsible for the novel STEP20 and STEP61 sequences was determined in the mouse STEP genomic DNA. We propose that the original STEP46, along with STEP20 and STEP61, are members of a brain-enriched subfamily of protein tyrosine phosphatases, and that STEP isoforms may have distinct functions within the central nervous system.