Summary 10.1002/9780470515655.ch9.abs The classical homology concept has served as a heuristic principle for organizing the enormous wealth of information on comparative anatomical patterns across a wide range of organisms. However, the classical homology concept reaches its limit as knowledge of the evolutionary, genetic and developmental processes that underlie these anatomical patterns increases. The biological homology concept places the known anatomical patterns into a mechanistic context and asserts that character identity is based on common variational properties. In this chapter a research programme for testing the biological homology concept that involves the following steps is outlined: (1) identifying of two or more putative homologues in a clade; (2) determining the phylogenetic distribution of the putative homologues; (3) describing the intra- and interspecific variation patterns of each putative homologue; (4) describing the development of each putative homologue, and determining if modes of development and distribution of homologues are phylogenetically congruent; and (5) providing and testing a model of how differences in modes of development between putative homologues effect differences in variational tendencies. The goal is to demonstrate a link between developmental and variational differences of two homologues.