The growing use of genetically engineered (GE) mice in scientific research has raised many concerns about the animal welfare of such mice. The types of welfare concerns may differ within the three stages that comprise the establishment of GE animal models: development, production, and research use. The role and impact of the members of the research team on these concerns may also vary with each stage. To make both scientific and animal welfare decisions at each stage, it is necessary to have a thorough knowledge of the animal model-in this case, the phenotypic expression of the GE animal. Phenotype screening is the analysis of visible or measurable characteristics of an animal that result from the genotype and its interaction with the environment. Phenotypes expressed that are relevant to the research program are usually carefully investigated; however, those that may have an impact on the animal's welfare but have little or no impact on the disease process under study are often less carefully studied. Thorough analysis and documentation of the animal welfare aspects of phenotype provide the research team with the information they need to control the environment to minimize negative animal welfare effects. Such information is also essential to allow members of the institutional animal care and use committee to perform necessary cost:benefit ethical review of proposed GE animal studies. Investigators who submit information about models for publication should document all aspects of a phenotype, including the area of scientific interest as well as those areas that affect animal welfare, for clarity and for subsequent research with the respective models.