Intact protein complexes can be separated by apparent molecular mass using a standard polyacrylarnide gel electrophoresis system combining mild detergents and the dye Coornassie Blue. Referring to the blue coloured gel and the gentle method of solubilization yielding native and enzymatically active protein complexes, this technique has been named Blue-Native Polyacrylarnide Gel-Electrophoresis (BN-PAGE). BN-PAGE has become the method of choice for the investigation of the respiratory protein complexes of the electron transfer chains of a range of organisms, including bacteria, yeasts, animals and plants. It allows the separation in two dimensions of extremely hydrophobic protein sets for analysis and also provides information on their native interactions. In this review we discuss the capabilities of BN-PAGE in proteornics and the wider investigation of protein:protein interactions with a focus on its use and potential in plant science.