Molecular beam epitaxy (MBE) has been developed over the past decade into one of the most versatile techniques for generating thin film semiconductor device structures. This development has been assisted by the use of low energy (0.1–10 keV) ion beams in a number of areas such as substrate surface preparation, film doping, metal-semiconductor contact formation and in situ surface analysis by secondary ion mass spectrometry and Auger depth profiling. Illustrative examples of the applications of ion beams in these areas are given. The use of ion beams in MBE has led to the discovery and exploration of a number of side effects of ion beams on semiconductor surfaces. These include group III metal surface segregation on III–V compound semiconductors, surface n-type channel formation on some III–V and II–VI compound semiconductors and II–VI alloy composition gradation. Some of these effects have been made use of in device structures. Mechanisms responsible for the effects are discussed and future trends in the use of ion beams in MBE are considered.