Endophenotypes are traits that, while genetically related to an illness, are not used for diagnoses (e.g., a symptom). It is unlikely that specific genes directly code for any of our current psychiatric diagnoses. Rather, genes influence neurobiological processes that either increase or decrease risk for mental illness. One use of an endophenotype is to help characterize a genetic locus or gene previously identified as conferring risk for a particular illness. In this context, endophenotypes help to bridge the gap between a behavioral syndrome and molecular genetic variation. Alternately, endophenotypes can be used for novel locus or gene discovery, particularly when used in multivariate analyses. In this chapter, we define endophenotypes and describe different ways they have been applied to aid our understanding of the genetic architecture of psychiatric disorders.