Inhibition of focal adhesion kinase (FAK) delays transendothelial migration of breast cancer cells. Here we investigate whether phosphorylation of specific tyrosine residues of FAK (397, 861, and 925) known to control aspects of cell migration on extracellular matrix (ECM), are also involved in transendothelial migration. AU-565 and MDA-MB-231 cells expressing Phe397 FAK show delayed or decreased transendothelial migration, demonstrating the involvement of the FAK autophosphorylation site. Only MDA-MB-231 cells expressing Phe861 FAK exhibit delayed transendothelial migration. Neither MDA-MB-231 nor AU-565 cells expressing Phe925 FAK show a change in transendothelial migration compared to untreated cancer cells. These findings suggest that modified signaling mechanisms regulate cancer cell migration through an endothelial monolayer versus those involved in cell migration on or through ECM.