A survey of copia (retroviral-like element) expression in flies representing 37 populations worldwide of Drosophila melanogaster, Drosophila simulans and Drosophila mauritiana demonstrates that, although copia elements are present in all three species, copia-encoded transcripts are detectable only in D. melanogaster. Levels of copia transcripts vary nearly 100-fold among flies representing geographically diverse populations of D. melanogaster and this variation is not correlated with variability in copia copy number. Analysis of transcript levels in interpopulation hybrids demonstrates that much of this variability may be attributable to the action of trans-acting controls. The geographic and phylogenetic pattern of copia expression suggests that moderate to high levels of copia expression may be a relatively recent evolutionary acquisition. The potential evolutionary significance of these findings is discussed.