This paper reviews recent advances in the application of transmission electron microscopy to the evaluation of structures, interfaces and defects in compound semiconductor thin films. It has been shown microscopically for the first time that the growth of (GaAs)m/(GaP)n strained layer superlattices by atomic layer epitaxy proceeds in a precisely layer-by-layer manner. Detailed characterizations of interfaces and defects in AlAs, GaAs and GaP on Si, also GaAsSb and Fe-doped InP on InP are described; later, the mechanisms which generate such defects and techniques for their elimination are discussed. Studies of atomic ordering in InGaP and InGaAs are presented, with reference to the mechanisms which generate ordered structures and their influence on the properties of the material.