Monoclonal antibodies to murine vascular cell adhesion molecule-1 (VCAM-1, CD106) revealed not only the expected VCAM-1 molecule with an apparent molecular weight of 100 kDa, but also a molecule with a smaller size of 46 kDa in stromal cells and stimulated endothelial cells. Peptide mapping suggested the 46 kDa and 100 kDa proteins were closely related. The 46 kDa, but not 100 kDa protein, was cleaved from the cell surface with phosphatidylinositol-specific phospholipase C (PI-PLC), showing that the 46 kDa protein was a GPI-linked molecule. The 46 kDa and 100 kDa isoforms of VCAM-1 were shown to be N-glycosylated, have similar kinetics of biosynthesis, and to be partially shed from the cell surface with a slight reduction of size. TNF-alpha induced both isoforms of VCAM-1 with a similar time course of appearance on the surface of endothelial cells. The relative amounts of the 46 kDa and 100 kDa isoforms depended on the cell type examined. The GPI-anchored isoform is functionally important, because on a cell on which it was expressed almost as well as the 100 kDa isoform, treatment with PI-PLC reduced VLA-4-dependent conjugate formation.