In search for materials for intermediate temperature solid oxide fuel cells, (Pr/Gd)BaCo2O5.5 is investigated by first principles calculations. Antisite defects are considered as they may modify the electronic and O diffusion properties but are rarely studied in double perovskite oxides. Octahedrally coordinated Co atoms are shown to realize intermediate and high spin states for PrBaCo2O5.5 and GdBaCo2O5.5, respectively, while pyramidally coordinated Co atoms always have high spin. It turns out that O vacancy formation is significantly easier in PrBaCo2O5.5 than in GdBaCo2O5.5, the difference in formation energy being hardly modified by antisite defects. While pyramidally coordinated Co atoms are not affected, we show that the presence of antisite defects causes parts of the octahedrally coordinated Co atoms to switch from intermediate to high spin.