Nearly all behavioral traits, ranging from personality traits such as neuroticism to schizophrenia and autism, are genetically influenced. With only minor exceptions, all are genetically complex—meaning that inheritance is not simply dominant or recessive or sex-linked, but follows more complex patterns indicative of more complex mechanisms. Most risk variants identified to date have only small effects on risk, and, in most cases, many risk variants at many risk loci interact with environmental factors to produce the phenotype. Such complexity has led to great challenges in increasing our knowledge of the inheritance of behavioral traits. Recent methodological advances have provided an improved set of tools that has led to advances in our understanding of the genetic influences on a range of behavioral traits. This chapter examines some of the issues involved that tend to make this a difficult problem and some of the solutions now being employed to approach those problems.