Layered-type ordering and oxygen vacancies ordering are revealed in GdBaMnFeO(6-δ) perovskite. Selected area electron diffraction and high-resolution transmission electron microscopy results indicate a modulation of the crystal structure. Ba and Gd ordering in (001)(p) layers is confirmed by high angle annular dark field scanning transmission electron microscopy and electron energy-loss spectroscopy. These techniques also revealed formation of layer-stacking defects in the crystals. Direct imaging of the oxygen sublattice is obtained by phase image reconstruction. Location of the oxygen vacancies in the (GdO)(x) layers is achieved by analysis of the intensity of the averaged phase image. Physical properties of the GdBaMnFeO(6-δ) perovskite, are likely to be strongly affected by its ordering effects and crystal microstructure. In this sense, layered-type GdBaMnFeO(6-δ) perovskite show better electrochemical properties as cathodes in SOFCs than ion disordered Gd(0.5)Ba(0.5)Mn(0.5)Fe(0.5)O(3-δ) perovskite.