The crystal structure of RuSr 2 GdCu 2 O 8 was successfully refined in the orthorhombic system (Pbam space group) using synchrotron powder diffraction data collected on a high purity and low defect containing sample. The microstructures of selected samples submitted to different thermal treatments were investigated by means of TEM analysis: the progressive annealing in an O 2 atmosphere suppresses the formation of nano-domains and extended planar defects, whereas annealing under vacuum favours the formation of extended planar defects and nano-domains as well. Lattice parameters increase with the anneling time, whereas an abrupt decrease of the c parameter occurs after de-oxygenation. A dependence of magnetization and superconductivity on the thermal treatment was evidenced and related to the structural and microstructural changes.