A large number of structural genomics programmes have been established worldwide with the common aim of large-scale, high-throughput protein structure determination. Due to the considerable challenges posed by the experimental methods of structural determination (primarily X-ray crystallography and nuclear magnetic resonance spectroscopy) it is important to select and prioritise candidate molecules that will maximise the information gained from each new structure. This paper describes the scientific principles that underlie target selection and the various bioinformatics tools that may be employed in such selection procedures. Then follows a discussion of the availability of resources incorporating these methods and a description of the design and application of a purpose-built target selection resource for structural genomics.