The body axis of vertebrates is an integrated cylinder of bones, connective tissue, and muscle. These structures vary among living and extinct vertebrates in their orientation, composition, and function in ways that render useless simplistic models of the selective pressures that may have driven the evolution of the axis. Instead, recent experimental work indicates that the vertebrate axis serves multiple mechanical functions simultaneously: bending the body, storing elastic energy, transmitting forces from limbs, and ventilating the lungs. On the biochemical level, research on human intervertebral discs has shown that collagens resist tension and torsion while proteoglycans bind water to resist compression. This molecular behavior predicts mechanical behavior of the entire joint, which, in turn helps determine the mechanical behavior of the vertebral column. The axial skeleton, in turn, is reconfigured by axial muscles that work by way of three-dimensional connective tissues that derive mechanical advantage for the muscle force by using the skin to increase leverage. Models may eventually help determine which evolutionary changes in the vertebrate body axis have had important functional and possibly adaptational consequences. Current reconstruction of the hypothetical stem lineage of early chordates and vertebrates suggests that the gradual mineralization of the vertebral elements, appearance of fin rays and new median fins, and transverse and then horizontal segmentation of the axial musculature are all features correlated with increases in swimming speed, maneuverability, and body size.