The unique geometry of multilayer thin films, with layer thicknesses on the nanoscale, gives rise to a wide range of novel properties and behavior that are not observed in the bulk. The novel behavior is critically dependent on the microstructure of the films. This paper reviews the use of a range of transmission electron microscopy (TEM) techniques to elucidate the structure, chemistry, and properties of multilayer thin films. The paper includes a brief introduction to the technological applications to which multilayer thin films are suited, followed by a description of the various TEM techniques. The final section of the paper presents the application of these techniques to various multilayer thin film systems.