The available methods for the separation of membrane proteins and lipoproteins are sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS/PAGE), followed by immunoblotting, isoelectric focusing (IEF), capillary electrophoresis (CE) and high‐performance liquid chromatography (HPLC). In this article it is shown that HPLC techniques, given their wide versatility, relative ease of use, and high resolution, may be considered the most valuable tool for the characterization of virtually any hydrophobic protein. Moreover, HPLC is not a destructive technique and therefore proteins, once separated, are available for further analytical investigations. Application examples are described and comparisons with other methods are discussed.