Summary: Tissue-specific gene ablation is accomplished by combining conventional gene targeting approaches with site-specific recombinases such as the Cre/loxP system. Despite the use of a cardiac-specific rat myosin light chain II promoter, our transgenic line (CRE3) had little or no Cre expression in the heart; however, strong Cre activity was detected in the brain as early as gestation day E11.5. This was determined by several methods including crossing our mouse line with a lacZ indicator line (ROSA26). Transgenic Cre, in this mouse line, mediated DNA recombination of loxPflanked genes selectively in neurons throughout the gray matter of the brain, cerebellum, spinal cord, as well as retina, dorsal, and sympathetic ganglia. Cre protein was also detected by immunohistochemistry exclusively in neurons, but not in other types of cells or tissues. Thus, our transgenic CRE3 mice provide pan-neuronal expression of CRE for carrying out conditional deletion of genes in neurons and their progenitors. genesis 42:6-16, 2005.