Mouse Phenotypes: A Handbook of Mutation Analysis, Second Edition, provides a road map for such analysis. Advice and practical guidance are provided, starting with the planning stages of gene targeting, CRISPR-Cas gene editing, or mutagenesis experiments, through the complete analysis of complex phenotypes, including tips on breeding strategies, studying dominant mutations, and characterizing a mutant mouse with no apparent phenotypic abnormalities. A systematic approach to the analysis, complemented with simple protocols, will help users make a comprehensive assessment of a particular phenotype resulting from a mutation and determine the timing and likely causes of specific developmental failures. Investigators using the laboratory mouse in genetic studies designed to understand mammalian biology will benefit from the authors' experience and advice in analyzing mutant phenotypes.