Transgenic experimentation yields insights that could not be perceived otherwise among populations of mammalian organisms (reviewed in references 1 and 2). However, information gained may, on occasion, be somewhat limited should germline gene dysfunction be deleterious in embryonic development, thereby precluding analyses in various somatic compartments of the adult organism. The production of chimeric mice bearing genetic mutations specifically in various somatic cells allows the study of gene function in physiologic contexts that would otherwise be unavailable or lethal. One elegant cell type-restricted chimeric approach has been the use of the RAG 2-null embryos as recipients in gene-targeted embryonic stem (ES) 1 cell–derived lymphoid development (3). While a lack of cell or tissue development may result from ES cell clonal variation, use of multiple ES clones and complementation by gene transfer allow for controlled studies. Some considerations remain the inability to direct genetic variation to multiple, experimentally defined cell lineages and the potentially unique nature of each chimeric mouse generated. Since inception, gene transfer experimentation has been generally limited to irreversible modifications of chromosomal DNA. Isolation of cells having undergone site-specific exchange or deletion of DNA sequence has only recently been developed using novel screening strategies for often low frequency events. To develop methods allowing high frequency site-specific chromosomal DNA modification, several laboratories have been investigating the activities of DNA recombinase enzymes to provide for additional experimental control over gene transfer and resulting mutagenesis among cell populations. Among the integrase family of recombinases, one of current relevance is termed Cre and exists as a 30-kD enzyme encoded within the genome of bacteriophage P1 (4). Recombination by Cre excises DNA residing between direct repeats of a 34-bp DNA substrate termed loxP. Cre recombination does not require ATP or topoisomerase activity (5) and has been found to function in heterologous eukaryotic genomes, includ-