As the brain develops, progenitor cells acquire the features of specific neuronal or glial subtypes through dynamic expression of the fate-determining signaling molecules and their targeting transcription factors. An effective and versatile approach for tracing lineage of progenitors into adult cell types is to target the promoter of an interested gene with Cre (a phage DNA recombinase) to achieve simultaneous activation during neurogenesis. The bacterial artificial chromosome (BAC) is an efficient Cre carrier. Not only the targeted gene remains diploidy in BAC-Cre transgenic mice, but also the large portions of the gene's regulatory elements to be incorporated in the BAC allow Cre to sufficiently and reliably reproduce the endogenous gene expression pattern. When the BAC-Cre mouse is crossed to a Cre reporter mouse, even Cre is transiently expressed. Cre-loxP mediated recombination can permanently activate a reporter gene, such as green fluorescent protein (GFP) in all lineage cells of the gene. Experimental designs and procedures for RecA-based BAC DNA modification and preparation for pronuclear injection are highlighted. Suggestions for the use of BAC-Cre transgenic mice in fate-mapping analyses are also provided.