New 3-amidinophenylalanine-derived matriptase inhibitors were developed and tested against the related trypsin-like serine proteases matriptase-2, thrombin and factor Xa. The strongest matriptase inhibition was found for compounds containing an N-terminal 2′,4′-dichloro- or 2′,4′-dimethoxy-biphenyl-3-sulfonyl group. The combination with a C-terminal piperidyl-cyclohexylurea residue provided the first monobasic matriptase inhibitor with a K_i value < 3 nM and excellent selectivity over thrombin. The X-ray structure of a representative analogue in complex with thrombin superimposed with matriptase provides information regarding the selectivity profile observed in this study.