PECAM-1 (CD31) is a cell adhesion molecule that is highly expressed at the sites of endothelial cell-cell contact and at lower levels on the surface of platelets and leukocytes. It is a member of the immunoglobulin gene superfamily and undergoes alternative splicing to generate several isoforms that differ only in their cytoplasmic domains. The tissue distribution of the expression of different PECAM-1 isoforms has not been previously defined. We have examined PECAM-1 expression in various mouse tissues and endothelial cells. PECAM-1 mRNA was highly expressed in lung, heart, and kidney, and to a lower extent in brain and liver. Most endothelial cells in culture expressed high levels of PECAM-1 mRNA; however, normal mouse brain endothelial cells rapidly lost PECAM-1 expression in culture. To examine the tissue distribution of PECAM-1 isoform expression, RT/PCR was performed on the RNA isolated from various mouse tissues and mouse endothelial cells. Cloning and sequencing of the cDNA products indicated that most tissues and endothelial cells expressed several PECAM-1 isoforms at different frequencies. The PECAM-1 isoform that lacks exons 14 and 15 was most frequently detected in all cases. A novel PECAM-1 isoform that lacks exons 12 and 14 was detected in brain. An antibody to the extracellular domain of PECAM-1 reacted with two major bands, at 130 kDa and 110-120 kDa, in lysates prepared from endothelial cells or kidneys at different stages of development. An antibody prepared against PECAM-1 exon 14, which reacts only with cytoplasmic domain of PECAM-1 isoforms that contain exon 14, failed to react with the major lower molecular weight form of PECAM-1 in these lysates. Therefore, PECAM-1 isoforms that lack exon 14 are expressed in endothelial cells and tissues in developmentally regulated fashion. These results illustrate that multiple PECAM-1 isoforms are expressed in various mouse tissues and endothelial cells. Understanding the distribution of PECAM-1 isoforms, and the identity of intracellular proteins with which they may interact, will help to elucidate the role of PECAM-1 in endothelial cell-cell interactions and morphogenesis.