This review focusses on the characterization of proteins of particular pharmaceutical interest as well as the selection and optimization of methods used in characterizing the drug substance and in Quality Control of the final product. Analytical methods, with illustrations where possible from recent developments in the field, are described. An overview of protein structure summarizes their spatial and temporal complexity, an appreciation of which is essential for thorough understanding of the methods of analysis. Electrophoresis and chromatography are described, emphasizing their utility in detection and quantitation of impurities or altered forms of product. Methods are described for the determination of the primary, secondary and complete structure of proteins, as well as other physical methods of characterization. Finally, applications of biological and immunological methods for analysis of activity and purity, respectively, are reviewed.