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A new type of phase separation in the polyelectrolyte solutions consisting of several types of charged macromolecules differing in their degree of ionization is presented. Via a general thermodynamic consideration we show that even a small difference in the degree of ionization of otherwise equivalent high‐molecular components results in their spatial separation occurring upon decreasing the temperature much earlier than precipitation of any of the pure components from the solution. Some implications of charge fractionation are discussed, including the separation of DNA (or RNA) strands interacting with different proteins and the appearance of heterogeneities in polyelectrolyte solutions of partially charged hydrophobic chains with polydispersed charge distributions such as sodium polystyrene sulfonate. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 3003–3009, 2007