The trypsin-like serine protease hepatocyte growth factor activator (HGFA) undergoes proteolytic activation during blood coagulation, result-ing in a 34 kDa ‘short form’, consisting mainly of the protease domain. The crystal structures of the recombinantly expressed HGFA ‘short form’ discussed herein have provided molecular insights into its interaction with inhibitors and substrates, as well as the regulation of catalytic activity.