Gene expression profiles of thousands of genes can now be examined en masse through cDNA and oligonucleotide microarrays. However, present applications of microarray technology do not include the study of gene expression from individual cell types residing in a given tissue/organ. This kind of resolution is absolutely necessary if one wants to generate hypotheses regarding mechanistic interactions between different cell types. We have previously demonstrated that by integrating laser capture microdissection (LCM) with DNA chips one can obtain cell type gene expression profiles (Luo et al., Nature Medicine, 5, 1999, 177–122). We present details of how we are using LCM to obtain cell-type specificity by giving examples within the brain and peripheral tissues. In addition, we will demonstrate the use of cluster analysis for the identification of genes whose expression is co-ordinated within specific cell types.