The accurate detection of a marker gene is fundamental to the assessment of any gene delivery protocol. The use of E. coli lacZ as such a marker gene has become common in studies on gene transfer to the central nervous system. The straightforward histochemical assay that is available to detect the gene product, beta-galactosidase; has made it an attractive system. However, using standard protocols, we have found dramatic non-E. coli lacZ staining in cells with neuronal, glial and endothelial morphology in the normal, adult rat brain. This false staining is primarily in the brainstem, but is evident in cortical and subcortical regions as well. This endogenous reactivity is independent of substrate concentration within the range tested, but is exquisitely sensitive to even small fluctuations in pH. In light of these findings, one must carefully examine any findings of E. coli lacZ gene expression in the rat brain based solely on histochemical analysis of tissue sections.