In Drosophila melanogaster, the genetic and molecular bases of post-mating changes in the female's behavior and physiology are poorly understood. However, DNA microarray studies have demonstrated that, shortly after mating, transcript abundance of >1700 genes is altered in the female's reproductive tract as well as in other tissues. Many of these changes are elicited by sperm and seminal fluid proteins (Acps) that males transfer to females. To further dissect the transcript-level changes that occur following mating, we examined gene expression profiles of whole female flies at four time points following copulation. We found that, soon after copulation ends, a large number of small-magnitude transcriptional changes occurred in the mated female. At later time points, larger magnitude changes were seen, although these occurred in a smaller number of genes. We then explored how four individual Acps (ovulin, Acp36DE, Acp29AB, and Acp62F) with unique functions independently affected gene expression in females shortly after mating. Consistent with their early and possibly local action within the female, ovulin and Acp36DE caused relatively few gene expression changes in whole bodies of mated females. In contrast, Acp29AB and Acp62F modulated a large number of transcriptional changes shortly after mating.