The development of marine renewable energy, including wave and tidal stream power, is a high priority for the Scottish Government. The environmental aspects of the licensing process has been brought together under a single Government body, Marine Scotland. Licensing requires that consideration is given to the requirements of the EU Habitats Directive, and this commonly leads to the need for an Appropriate Assessment of the potential risk to populations of protected species (notably grey and common seals) from collision with rotating turbines. An approach is described which combines a model of the foraging behaviour of seals with the probability of seals being damaged by passing through the volume of water swept by a turbine. The acceptability of the estimated potential mortality is assessed against an estimated Potential Biological Removal (PBR) for the relevant populations. The scope for improvements in all aspects of the models is discussed as a guide to research and developmental needs.