This handook is intended as a resource for scientists who use Ion Beam Analysis (IBA), to help them understand and minimise beam damage induced during the analysis. The basic physics of ion-matter interactions, from the perspectve of damage induced by the beam during Ion Beam Analysis, is presented at a level suitable for post-graduate students. The specificities of damage induced in widely used IBA techniques such as Backscattering Spectrometry (RBS), Nuclear Reaction Analysis (NRA), Elastic Recoil Detection Analysis (ERDA) and Particle-Induced X-ray Emission (PIXE) are presented, followed by sections on damage induced during analysis of different classes of materials such as metals, semiconductors or polymers. A comprehensive bibliography is included.