Reversible phosphorylation of tyrosine residues plays a crucial regulatory role in various cellular events, including differentiation and proliferation of lymphocytes. Here, we report the isolation of a murine receptor-type protein tyrosine phosphatase (PTP), mRPTP-sigma, which is expressed in both immature thymocytes and stroma cells. At least two alternatively spliced transcripts of mRPTP-sigma (T and B) were observed. mRPTP-sigma T was the dominant form in the thymus and had three Ig-like and eight fibronectin type III-like domains in the extracellular portion. mRPTP-sigma T was almost identical with RPTP-sigma/PTP NE-3/PTP-P1/CPTP1, a PTP recently cloned from rat brain, except that RPTP-sigma/PTP NE-3/PTP-P1 was about 400 amino acids shorter than mRPTP-sigma T. mRPTP-sigma B, the second form of mRPTP-sigma, was dominant in the brain and was most likely the murine counterpart of RPTP-sigma/PTP NE-3/PTP-P1. In the developing thymocytes, the expression of mRPTP-sigma was high in double negative (CD4-CD8-), low in double positive (CD4+CD8+), and marginal in single positive (SP; CD4+CD8- or CD4-CD8+) subpopulations. No upregulation of mRPTP-sigma was observed in the spleen cells stimulated with Con A. Developmental regulation of mRPTP-sigma expression suggests its involvement in the control of T lymphocyte differentiation.