In the past few years, it has become apparent that there is a substantial amount of noncoding DNA that contributes to genome function. However, the multidimensionality of noncoding DNA properties does not allow us to readily identify, characterize, and assess the functional impact of mutations, polymorphisms, and interspecific substitutions. In this chapter, we discuss the evolutionary properties of some of the known noncoding genomic elements, namely regulatory regions, and the extensions of this to other potentially functionally important noncoding regions such as conserved noncoding regions. The implications of this analysis for studies looking at molecular phenotypes such as gene expression and whole-organism phenotypes (e.g., disease) are presented in the context of the exploration of noncoding DNA properties. The aim is to take advantage of current and emerging analysis methods for noncoding DNA to elucidate the genetic causes of phenotypic variation.