We have isolated a partial-length cDNA for bovine thrombomodulin from a lambda gt11 bovine adrenal capillary endothelial cell expression library. This was accomplished by immunoscreening with rabbit anti-thrombomodulin IgG heteroantibody and then rescreening with the initial positive recombinant insert. The cDNA obtained was authenticated by showing that it coded for the primary structure of two separate regions of bovine thrombomodulin. The nucleotide sequence of the largest cDNA allowed us to establish the structure of about 80% of the mature thrombomodulin transcript, which encodes the C-terminal half of the polypeptide. This membrane component is structurally similar to coated-pit receptors and is organized into domains that resemble those of the low density lipoprotein receptor.