Isomorphous difference methods allow rapid and detailed visualization of localized changes in macromolecular structures, whether as a result of mutation or the binding of ligands. Practical aspects of isomorphous methods and differential crystallography are presented, particularly in their application to the phasing of new structures by multiple isomorphous replacement and the detection and characterization of ligand binding. Techniques for maintaining isomorphism between crystals to maximize the differential signal are covered, as are the computational steps involved in generating difference electron density maps. Frontier applications such as determining single-site ligand-binding affinities crystallographically, high-throughput screening of combinatorial compound libraries, in crystallo competition assays, and inferring protein function via exogenous ligand-binding screens are discussed.