Embryonic stem (ES) cell technology has clearly established itself as a powerful technique for the examination of gene function in vivo. The vast majority of gene-targeting experiments to date have been designed simply to inactivate the function of the gene of interest by the targeted insertion of a selectable marker into the ES genome. Homologous recombinant ES cells are used without further modification for the generation of mice that bear a permanently modified allele in all cells from the onset of development. In contrast to this “conventional” gene-targeting strategy, in recent years, the use of the Cre/loxP recombination system in conjunction with gene targeting has greatly expanded the versatility and avenues with which biologic questions can be addressed in the mouse. In addition to the generation of subtle mutations, this system allows for a number of other genotypic options in ES cells or mice by strategically incorporating Cre recombinase recognition (loxP) sites into the genome and the subsequent expression of recombinase in vitro or in vivo. In particular, when Cre is expressed in mice harboring a loxP-containing target gene, the desired gene modification can be restricted to certain cell types or developmental stages of the mouse (conditional gene targeting) depending on the tissue specificity and timing of recombinase expression. There is no definitive rule to decide whether, for a particular experiment, conventional or conditional gene targeting is more appropriate since this depends on the specific biologic question and the peculiarities of the gene studied.