The nature of an organism is defined by the genes that it expresses. Genome- and expressed-sequence-tag (EST) sequencing projects are underway for many of the major parasites of humans and animals. These provide essential datasets that delineate the genes present in an organism and, in the case of ESTs, some quantitative information on gene expression. The temporal and quantitative analysis of gene expression is essential to fully exploit these datasets and define the biology of the parasite at the molecular level. Here, we discuss the application of serial analysis of gene expression (SAGE) for this purpose. SAGE is a technique that allows the rapid, quantitative analysis of thousands of transcripts. It complements microarray analysis with the advantage that it is affordable for standard laboratories. It provides a platform to define complete metabolic pathways and has been applied to study responses to drug treatment and the molecular events that are associated with arrested larval development.