Single-chain urokinase (SC-UK) has an intrinsic amidolytic activity, as measured with synthetic substrate (Kabi S-2444; pyro-Glu-Gly-Arg-pNitroanalide), which was found to be 0.1% to 0.2% that of its plasmin-activated derivative, two-chain UK (TC-UK). A study of the reaction of SC-UK with plasminogen is complicated by the effect of the reaction product, plasmin, on both reactants. The resultant generation of TC-UK and Lys-plasminogen produces secondary reactions which greatly augment plasminogen activation. To confine enzymatic activity to the primary reaction, after pretreatment to eliminate trace TC-UK contaminants, SC-UK was incubated with Glu- or Lys-plasminogen in the presence of aprotinin (500 KIU/mL) to inhibit generated plasmin and dansyl-glutamyl-glycyl-arginyl-chloromethylketone (20 mumol/L), which irreversibly inhibited TC-UK but not SC-UK. Analysis by reducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed a plasminogen-activating activity for SC-UK that was approximately 0.4% that of TC-UK. Both SC-UK and TC-UK preferentially activated Lys-plasminogen over Glu-plasminogen. Similarly, Glu-plasminogen activation was augmented by lysine or soluble fibrin. The ratio of the reaction rates of SC-UK and TC-UK were comparable for Glu- and Lys-plasminogen. It is concluded that there is a major difference in the catalytic activities of SC-UK and TC-UK against plasminogen that is comparable to that against synthetic substrate.