Human granzyme H (GzmH) is constitutively expressed in human NK cells that have important roles in innate immune responses against tumors and viruses. GzmH is a chymotrypsin-like serine protease. Its substrate preference and its mechanism of substrate recognition are poorly understood. To provide structural insights into the substrate recognition mechanisms for GzmH, we solved the crystal structures of a D102N-GzmH mutant alone and in complex with a decapeptide substrate and an inhibitor to 2.2 Ă
, 2.4 Ă
, and 2.7 Ă
, respectively. The Thr189, Gly216, and Gly226 specificity triad in the S1 pocket of GzmH defines its preference for bulky, aromatic residues (Tyr and Phe) at the P1 position. Notably, we discovered that an unusual RKR motif (Arg39-Lys40-Arg41), conserved only in GzmH, helps define the S3Ⲡand S4Ⲡbinding regions, indicating the preference for acidic residues at the P3Ⲡand P4Ⲡsites. Disruption of the RKR motif or the acidic P3Ⲡand P4Ⲡresidues in the substrate abolished the proteolytic activity of GzmH. We designed a tetrapeptide chloromethylketone inhibitor, Ac-PTSY-chloromethylketone, which can selectively and efficiently block the enzymatic and cytotoxic activity of GzmH, providing a useful tool for further studies on the function of GzmH.