The complex anatomical organization and cellular heterogeneity of the mammalian brain may complicate the interpretation of transcriptome analysis of brain tissues. In the April 24 Proceedings of the National Academy of Sciences, Zirlinger et al. describe how in situ hybridization studies can improve microarray analysis of the brain (Proc Natl Acad Sci USA 2001, 98:5270-5275). The authors compared the expression of over 34,000 genes using Affymetrix GeneChip oligonucleotide arrays with RNA from five different anatomical regions dissected from mice brains. About 1.3% of the genes analysed were enriched in only one of the five regions. Subsequent in situ hybridization was used to confirm the microarray results. About 60% of genes were consistent with microarray analysis, 20% gave no signal, and 20% were not enriched or inconsistent with microarray results. The amygdala region is involved in emotional behaviours and has been anatomically divided into 13 subregions. When Zirlinger et al. examined some of the 33 amygdala-enriched genes, they found that 75% were expressed in restricted subregions. This report highlights the benefits of using in situ hybridization to validate microarray results.