The miniaturisation of technology increasingly requires the development of both new structures as well as novel techniques for their manufacture and modification. Semiconductor nanowires (NWs) are a prime example of this and as such have been the subject of intense scientific research for applications ranging from microelectronics to nano-electromechanical devices. Ion irradiation has long been a key processing step for semiconductors and the natural extension of this technique to the modification of semiconductor NWs has led to the discovery of ion beam-induced deformation effects. In this work, transmission electron microscopy with in situ ion bombardment has been used to directly observe the evolution of individual silicon and germanium NWs under irradiation. Silicon NWs were irradiated with either 6 keV neon ions or xenon ions at 5, 7 or 9.5 keV with a flux of 3 × 1013 ions cm−2 s−1. Germanium NWs were irradiated with 30 or 70 keV xenon ions with a flux of 1013 ions cm−2 s−1. These new results are combined with those reported in the literature in a systematic analysis using a custom implementation of the transport of ions in matter Monte Carlo computer code to facilitate a direct comparison with experimental results taking into account the wide range of experimental conditions. Across the various studies this has revealed underlying trends and forms the basis of a critical review of the various mechanisms which have been proposed to explain the deformation of semiconductor NWs under ion irradiation.