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(111)-Fe3O4/CoO multilayers grown by molecular-beam epitaxy, deposited on sapphire (0001) substrates, exhibit an unexpected high-angle θ–2θ X-ray diffraction spectrum. The even-order Fe3O4 main Bragg peaks, nearly coinciding with the CoO Bragg peaks, clearly show multilayer splitting, whereas this is absent for the odd-order Fe3O4 peaks. This effect is shown to originate from a small discrete fluctuation of the CoO layer thickness. The system under study exemplifies the marked effect of discrete interfacial disorder in multilayers in which one of the components has a lattice parameter nearly matching twice the lattice parameter of the other component.