The ability to interrogate gene expression levels of an organisms entire transcriptome has provided researchers with a powerful tool. This power has been brought to bear on biological questions in the areas of development, aging, cell biology, disease models, stress and toxicology. Many novel insights into biological processes have been obtained from these studies and have led to connections to other systems level approaches including RNA interference and bioinformatics. In this article, we review microarray studies that have used the nematode Caenorhabditis elegans. Specific considerations of C. elegans as a model organism in this context are derived and inferences based on combining microarray data sets with other model organisms are presented and discussed. Sources for obtaining microarray data as well as the microarrays themselves are listed. Finally, we take a look into the future of this remarkable and still evolving field of expression profiling in C. elegans.