Gene expression is controlled by a complex network of molecular interactions. Genetic changes that alter this network contribute to phenotypic differences within and between species. To better understand how mutation and selection affect the evolution of gene expression, we have investigated properties of new mutations that create regulatory variation in Saccharomyces cerevisiae and compared their effects to those of regulatory variants segregating in the wild. Comparisons between these two datasets are providing are being used to make inferences about how regulatory networks evolve. Genetic variation segregating within a species reflects the combined activities of mutation, selection, and genetic drift. In the absence of selection, polymorphisms are expected to be a random subset of new mutations; thus, comparing the effects of polymorphisms and new mutations provides a test for selection. When evidence of selection exists, such comparisons can identify properties of mutations that are most likely to persist in natural populations. We have been investigating how mutation and selection contribute to variation in cis- and trans-regulatory sequences controlling gene expression by empirically determining the effects of new mutations and polymorphisms in Saccharomyces cerevisiae