Changes in gene expression are an important source of phenotypic variation. During the last decade, various methods have been developed for quantifying levels of gene expression (mRNA abundance) on a genomic scale in diverse organisms. Application of these techniques has shown that variation in gene expression is common both within and between species. These expression differences can arise from cis- and/or trans-regulatory changes, and methods are now available for distinguishing between them. Using such approaches to compare the genetic basis of polymorphic and divergent expression in flies (Drosophila) and yeast (Saccharomyces) has shown that cis-regulatory changes account for a greater proportion of expression differences between than within species. In this talk, I will use analysis of gene expression in closely related Drosophila species to illustrate this and other patterns of regulatory evolution and then show how quantifying properties of new regulatory mutations (in S. cerevisiae) is providing insight into the evolutionary processes responsible for these patterns.