This review provides an overview of animal models for the evaluation, comparison, and systematic optimization of tissue engineering and regenerative medicine strategies related to bone tissue. This review includes an overview of major factors that influence the rational design and selection of an animal model. A comparison is provided of the 10 mammalian species that are most commonly used in bone research, and existing guidelines and standards are discussed. This review also identifies gaps in the availability of animal models: (1) the need for assessment of the predictive value of preclinical models for relative clinical efficacy, (2) the need for models that more effectively mimic the wound healing environment and mass transport conditions in the most challenging clinical settings (e.g., bone repair involving large bone and soft tissue defects and sites of prior surgery), and (3) the need for models that allow more effective measurement and detection of cell trafficking events and ultimate cell fate during the processes of bone modeling, remodeling, and regeneration. The ongoing need for both continued innovation and refinement in animal model systems, and the need and value of more effective standardization are reinforced.