Atomic resolution Z-contrast imaging and electron energy-loss spectroscopy (EELS) were used to study the defect structure of oxygen deficient strontium cobaltite (SrCoO3-delta) after repeated oxidation/reduction cycles at elevated temperatures. Ordered microdomains were found in the reduced sample. Z-contrast imaging showed ordering in alternate CoO2 planes, characteristic for a brownmillerite-type vacancy ordered structure. EELS showed that the average valence state of cobalt had decreased after testing. In the tested sample, cobalt was found in + 3 and + 2 valence states, respectively. In addition, cobalt oxide precipitates were found at grain boundaries and in triple pockets in this sample, indicating a cobalt deficiency of the grains. The mechanisms for the formation of the observed microstructure are discussed.