Microstructural studies of Si‐Si interfaces grown by molecular beam epitaxy reveal pockets of oxygen‐rich material for certain substrate preparation conditions. For Czochralski substrates which are cleaned using an argon ion sputtering technique, a high density (about 1011/cm2) of oxygen‐rich pockets about 30 A˚ in size is observed using cross‐sectional transmission electron microscopy and x‐ray microanalysis for short (less than about 15 s) sputtering times. For longer sputtering times, no significant defect density is observed. Post‐deposition thermal annealing causes a dramatic increase in the density of oxygen‐rich defects, and it is suggested that this is due to trapping of oxygen which has diffused from the bulk of the substrate wafer. For (100) interfaces, no significant dislocation activity is associated with the defects, even for densities up to 1012/cm2. On (111) interfaces, however, a large planar fault density is observed. Ramifications for silicon homoepitaxy are discussed.