Fuel cells and, more particularly, the H2—Cl2 proton exchange membrane fuels cells are described. In some embodiments the fuel cells include a flow through electrolyte assembly that is configured to allow the introduction of a first (relatively dilute) electrolyte into the cell, and the remove of a second (relatively concentrated) electrolyte from the cell. Fuel cell stacks and systems for cogenerating electricity and hydrochloric acid using such fuel cells are also described.