Gene expression analysis provides an insight into the unique and defining biomolecular characteristics of a given cell type. However, heterogeneous cellular compositions hinder gene analysis studies from most tissue samples. The laser microdissection (LMD) technique allows for the unambiguous isolation of a desired cell population. However, preserving RNA integrity can be challenging because of the deliberately limited amount of starting material, sometimes as little as a single cell. General laboratory procedures for reducing ribonuclease (RNase) activity, both in reagents and in the laboratory environment, are required for successful downstream RNA isolation and quantitation. Quality RNA can be extracted from sections made from flash-frozen and paraffin-embedded tissue. The standard histological stains such as hematoxylin and eosin (H&E), or toluidine blue, can provide visualization of the cells of interest. Following LMD, validation of RNA integrity should precede downstream analysis.