It is shown by means of electron microscopy and electron diffraction that the "structural" vacancies in Ba2YCu3O7-δ undergo an order-disorder transformation accompanied by a change in symmetry from orthorhombic to tetragonal. A superstructure due to the ordering of vacancies was found in certain crystal parts; it leads to doubling of the a0 parameter. It is shown that the ordering of the vacancies is important for the superconducting behaviour. In order to obtain a high Tc supraconductor the final heat treatment is crucial.