The importance of homology in biology is widely acknowledged. Wake (1994: 284) writes that “[h]omology is the central concept for all of biology.” Patterson (1987: 18) observes that “all useful comparisons in biology depend on the relation of homology.” Whenever we ask if two characters are the same characters, we are asking if they are homologous, regardless of whether those characters are genetic, morphological, anatomical, or behavioral. Yet, like many central concepts in biology, our understanding of homology is plagued by unresolved questions. For example, how should we define “homology”? There is no agreed upon definition in the literature. Or, how do we explain the fact that two homologous characters can be caused by nonhomologous developmental factors (Hall 2007)? Or more fundamentally, what causes new homologues (Wagner 2001)? Then there are questions about the role of homologies in evolution. Homologues are quasi-independent, heritable units that selection acts on; they are units of evolvability (Laubichler 2000; Brigandt 2007). The idea of homologues as units of evolvability cries out for analysis. These are all pressing questions. But given space limitations, this article can only focus on two. One is the possibility of a unified theoretical account of homology. The other is how homologues at one hierarchical level are caused by nonhomologues at a lower level. As we shall see, recent work offers an emerging approach to homology that integrates phylogeny and development (Laubichler 2000). Such an approach provides the basis for a unified theoretical account of homology, and it sheds light on the hierarchical nature of homology.