For an ever-increasing number of species, the completed genomic sequence is available, providing a means to identify all the genes encoded in a genome. The functional relationships between these genes must be defined in order to generate a cohesive understanding of the molecular events that direct metazoan development. The model organism C. elegans, with its completed genomic sequence, defined cell lineage and robust genetics, provides an excellent opportunity to reconstruct the genetic relationships that underlie the development of a relatively simple animal. The change in expression of every predicted gene in the genome can be quantified under defined experimental conditions using DNA microarrays, thus providing a ”molecular signature“ of particular developmental processes. Because DNA microarray analysis does not rely upon detection of a gross morphological phenotype, genes whose function escapes identification in mutation screens can now be associated with different developmental processes. Together, C. elegans and DNA microarrays are a powerful combination with which to attack complex problems in developmental biology and work toward a more complete understanding of the underlying genetic networks governing development.