Inertial properties of animal bodies and segments are critical input parameters for biomechanical analysis of standing and moving, and thus are important for paleobiological inquiries into the broader behaviors, ecology and evolution of extinct taxa such as dinosaurs. But how accurately can these be estimated? Computational modeling was used to estimate the inertial properties including mass, density, and center of mass (COM) for extant crocodiles (adult and juvenile Crocodylus johnstoni) and birds (Gallus gallus; junglefowl and broiler chickens), to identify the chief sources of variation and methodological errors, and their significance. High-resolution computed tomography scans were segmented into 3D objects and imported into inertial property estimation software that allowed for the examination of variable body segment densities (e.g., air spaces such as lungs, and deformable body outlines). Considerable biological variation of inertial properties was found within groups due to ontogenetic changes as well as evolutionary changes between chicken groups. COM positions shift in variable directions during ontogeny in different groups. Our method was repeatable and the resolution was sufficient for accurate estimations of mass and density in particular. However, we also found considerable potential methodological errors for COM related to (1) assumed body segment orientation, (2) what frames of reference are used to normalize COM for size-independent comparisons among animals, and (3) assumptions about tail shape. Methods and assumptions are suggested to minimize these errors in the future and thereby improve estimation of inertial properties for extant and extinct animals. In the best cases, 10%-15% errors in these estimates are unavoidable, but particularly for extinct taxa errors closer to 50% should be expected, and therefore, cautiously investigated. Nonetheless in the best cases these methods allow rigorous estimation of inertial properties.