The elucidation of structural and electronic aspects of paramagnetic organic cofactors in their protein surroundings and related model compounds is a topic of widespread interest. In this field, electron paramagnetic resonance (EPR) spectroscopy, especially in conjunction with high-resolution electron-nuclear double resonance (ENDOR) is an important tool, allowing us to analyze details of the distribution of the unpaired electron spin, which is influenced by the interaction between the cofactor and its immediate environment, as well as to characterize paramagnetic intermediate states in the course of the protein action. In this account, investigations are reported in which EPR/ENDOR methods have contributed significantly to answering questions on mechanistic and structural aspects of protein function. Emphasis is given to in-depth characterizations of electronic and spatial structures of radical cofactors and their positioning relative to substrate molecules. After a brief introduction, covering some of the trends of modern EPR/ENDOR method development, we will focus, as examples, on characterizations of quinone-type and flavin cofactors in two proteins, (i) quinoprotein alcohol dehydrogenase, and (ii) DNA photolyase.