The importance of variation and evolution of gene expression during complex developmental processes is still relatively poorly understood. In an Advanced Online Publication in Nature Genetics Rifkin et al. describe a comparative genomics study that characterizes inter-species differences in gene expression during Drosophila metamorphosis (Nature Genetics, 27 January 2003, doi;10.1038/ng1086). Rifkin et al. used microarrays to measure genome-wide developmental changes in 12,866 genes at the onset of metamorphosis in four inbred strains of Drosophila melanogaster and strains of D. simulans and D. yakuba. Around 27% of genes differed significantly in the extent of developmental change between at least two lineages. Only about 1,000 genes changed significantly in all lineages. Rifkin et al. found that changes in the expression of genes encoding key transcription factors was relatively stable, whereas their downstream target genes show greater evolutionary changes in expression.