Localization of the plasminogen binding sites on fibrin has been difficult since these interactions occur on polymerizing fibrin, and studies with fragments can be misleading because of multiple carboxyl-terminal lysines that may bind to plasminogen. A hetero-functional photoaffinity cross-linker was used to study these interactions. Following attachment of the cross-linker to plasminogen in the dark, a clot was formed by addition of fibrinogen or fragment X and thrombin, and then the plasminogen was cross-linked to adjacent parts of fibrin by exposure to light. There was more Glu1-plasminogen bound to fibrin than to fibrinogen and more to fragment X polymer than to fibrin. Electron microscopy of rotary shadowed individual molecules reveals that Glu1-plasminogen appears to be more compact than Lys78-plasminogen or Glu1-plasminogen with 6-aminohexanoic acid. Cross-linked complexes from the dissolved clot observed by electron microscopy reveal plasminogen bound to the end of fibrin or bridging the ends of two fibrin molecules; larger complexes were also observed. Analysis of changes in the appearance of negatively contrasted fibers with plasminogen bound also indicates the probable locations of binding sites, yielding results consistent with the cross-linking studies. The photoaffinity probe was also used to study interactions between plasminogen and fibrin or its derivatives in the course of tissue plasminogen activator-mediated fibrinolysis. Samples cross-linked at various times indicate that complexes with fragment X are particularly dominant during the rapid phase of plasminogen activation. In conclusion, these studies indicate that plasminogen binds to the pocket at the end-to-end junction between two fibrin or fragment X molecules in the protofibril; from this position, it can reach all of the sites that are cleaved during fibrinolysis.