Defensins, cationic peptides with bacteriolytic properties, are abundantly found at inflammation sites and in human coronary vessels. Vascular occlusive diseases, such as myocardial infarction, pulmonary embolism, and peripheral arterial occlusion are presently treated by thrombolytic intervention using staphylokinase, a plasminogen activator of bacterial origin. In this study we assessed a possible interaction between defensins and staphylokinase, both molecules being present in an acutely ill patient. Using an ELISA-based system, we found that staphylokinase and defensins displayed a strong and dose-dependent binding. In contrast, urokinase, another plasminogen activator of endogenous origin, displayed only minimal binding to defensins. Next, we proved that interaction between staphylokinase and defensins led to fuctional consequences resulting in a significant decrease (p < 0.002) of plasminogen activation capacity upon complex formation. In contrast, urokinase retained most of its activity even in 10-fold molar excess of defensins. Finally, we found that staphylokinase-triggered lyrsis of fibrin was efficiently inhibited in the presence of defensins. To assess structural requirements for staphylokinase/defensin interaction, six staphylokinase mutant variants were studied. Inactivation pattern of the tested staphylokinase variants suggested a direct binding of defensins to serine protease-like domain of staphylokinase. In conclusion, we show complex formation between staphylokinase and alpha-defensins resulting in a significant reduction of fibrinolytic activity. This finding may have clinical implications, since fibrinolytic effects of staphylokinase may be downregulated at the site of vascular occlusion.