The revolution in our knowledge about the genomes of organisms gives rise to the question, what do we do with this information? The development of techniques allowing high throughput analysis of RNA and protein expression, such as cDNA microarrays, provide for genome wide analysis of gene expression. These analyses will help bridge the gap between systems and molecular neuroscience. This review discusses the advantages of using a subtractive hybridization technique, such as a representational difference analysis, to generate a custom cDNA microarray enriched for genes relevant to investigating complex, heterogeneous tissues such as those involved in the chemical senses. Real and hypothetical examples of these experiments are discussed. Benefits of this approach over traditional microarray techniques include having a more relevant clone set, the potential for gene discovery and the creation of a new tool to investigate similar systems. Potential pitfalls may include PCR artifacts and the need for sequencing. However, these disadvantages can be overcome so that the coupling of subtraction techniques to microarray screening can be a fruitful approach to a variety of experimental systems.