Protamines are polycationic proteins that are widely used for neutralisation of the anticoagulant action of heparin. However, several reports have shown adverse, mast cell-dependent reactions to protamine. The exact mechanism by which protamine causes these adverse effects is not clear. In the present study, the possibility that protamine may influence mast cell chymase function was investigated. Mast cell chymase is in vivo recovered in a macromolecular complex with heparin proteoglycan, and this interaction is essential for expression of optimal enzymatic activity. Protamine was shown to strongly reduce the activity of mast cell chymase by a mechanism that involved displacement of the chymase from heparin proteoglycan.