The genetic basis of variation in gene expression lends itself to investigation by microarrays. For genetic analysis, we view the expression level of a gene as a quantitative or 'complex' trait, analogous to an individual's height or cholesterol level, and, therefore, as an inherited phenotype. Several genetic analyses of 'gene expression phenotypes' have been carried out in experimental organisms, and initial steps have been taken toward similar studies in humans--although these present challenging technical and statistical problems. Further advances in the genetic analysis of variation in gene expression will contribute to our understanding of transcriptional regulation and will provide models for studying other quantitative and complex traits.