Prostasin is a trypsin-like serine protease that is glycosylphosphatidylinositol-anchored to the epithelial cell surface, from where it can be released in a soluble form. We undertook a co-expression search using the Genesis Enterprise System Database from Gene Logic to identify prostasin inhibitors, on the assumption that prostasin and its natural inhibitors may have a similar gene expression pattern. We found the expression profile of prostasin in normal human tissues to correlate highly with hepatocyte growth factor activator inhibitor-1B (HAI-1B) and its splice variant HAI-1. Soluble HAI-1B (sHAI-1B), comprising the entire extracellular domain, formed a 1:1 complex with purified prostasin in protein binding assays and inhibited prostasin enzymatic activity with an IC(50) of 66 +/- 15 nM. Two sHAI-1B mutants with inactivated N- and C-terminal Kunitz domains (KD1 and KD2) were used to show that the interaction of sHAI-1B with prostasin is mediated by KD1. In agreement, KD1 (Thr(246)-Val(303)) alone potently inhibited prostasin activity (IC(50) = 4.7 +/- 0.5 nM). Furthermore, prostasin was isolated with two major HAI-1/1B fragments (40 and 58 kDa) from OVCAR3 cell medium, demonstrating that prostasin.HAI-1/1B complexes are formed naturally. Moreover, when prostasin and HAI-1B were co-expressed in Chinese hamster ovary cells, complexes of prostasin with HAI-1B were detected on the cell membrane as well as in the culture medium, suggesting that preformed complexes were shed from the cell surface. The identification of HAI-1B as a potential physiological regulator of prostasin function, as described herein, may further the investigation of the role of prostasin in normal physiology and cancer.