Background: Hepatocyte growth factor activator inhibitor (HAI)-1 and HAI-2 may regulate matriptase trafficking and activation. Results: Ablation of endogenous HAI-2, but not HAI-1, causes loss of epithelial matriptase in vivo and in vitro, due to uncontrolled prostasin-dependent activation and shedding. Conclusion: HAI-2, but not HAI-1, regulates matriptase cell surface expression level. Significance: The study identifies HAI-2 as a principal regulator of prostasin-mediated matriptase activation.