Free-flow electrophoresis (FFE) exploits differences in the overall charge of bio-particles separating cells, organelles, macromolecules, ions, etc. according to their distinct electrophoretic mobility and isoelectric point (pI) values. Indeed, around a neutral pH organelles usually exhibit a negative surface charge, migrating in an electric field from the cathode toward the anode. Since its introduction more than five decades ago by Barrollier etal., Z. Naturforsch. 1958, 13b, 745-755 and Hannig, Z. Anal. Chem. 1961, 181, 244-254, FFE has become an established analytical and preparative separation method for the isolation of a variety of organelles. Particularly, in sophisticated, multistep separating processes to separate subpopulations of organelles, it has gained, meanwhile, a position as a versatile technology and essential element. Relying on the distinct surface charges instead of buoyant densities of cell organelles, the FFE technology is best supporting a preceding centrifugation-based fractionation of subcellular compartments in the second dimension. In the following review, the two-step isolation and purification of subpopulations of classic animal and plant cell organelles will be mainly exemplified.