The use of genetically engineered mice to understand gene function is widespread. Changes to the mouse genome can be introduced with gene targeting vectors or with transgenes. Targeting vectors are usually used to ablate gene expression while transgenes are designed to express proteins that are normally absent from the organism. For example, gene targeting in mouse embryonic stem cells can be used to generate a mutant mouse model that fails to express a physiologically important protein. Transgenes that express the missing protein or a substitute for the missing protein can be used to assess possible gene therapies for the mutant mouse. Both gene targeting and transgene approaches can be used to study regulatory elements that control gene function. Putative control elements can be added to or removed from the chromosome with targeting vectors. Transgenes carrying long DNA sequences that include different combinations of potential control elements can be introduced into the genome to assess their effects on gene expression. The exploration of how genes interact to control development, homeostasis, and pathophysiological conditions can be dissected by introducing carefully designed genetic constructs into model organisms.