Free-flow electrophoresis (FFE) is a technique for separation of proteins, peptides, organelles, and cells. With zone electrophoresis (ZE-FFE), organelles are separated according to surface charge. The plant Golgi and endoplasmic reticulum (ER) are similar in density and are therefore separated with difficulty using standard techniques such as density centrifugation. Purification of the ER and Golgi apparatus permits a biochemical and proteomic characterization which can reveal the division of processes between these compartments. Here we describe complete separation between the ER and more negatively charged Golgi compartments using ZE-FFE. We also describe techniques for assigning proteins to partially separated ER and the less negatively charged Golgi compartments.