The fyn proto-oncogene encodes a 59-kD membrane-associated protein-tyrosine kinase that is implicated in the control of cell growth. We report here that there are two distinct fyn-encoded transcripts that exhibit mutually exclusive expression patterns; one form is found in thymocytes, splenocytes, and some hematolymphoid cell lines, while a second form accumulates principally in brain. The thymocyte and brain forms of p59fyn differ in their kinase domains, and are generated by mutually exclusive alternative splicing of a single exon. Immunoprecipitation followed by in vitro autophosphorylation demonstrates that both forms of p59fyn are enzymatically active. Our results define a novel form of the p59fyn protein-tyrosine kinase, with an altered catalytic domain, that apparently participates in a specialized signal transduction pathway in hematopoietic cells.