Methods, systems, and apparatus, including computer-readable storage media, for surgical alignment using references. In one general aspect, a method includes coupling a guide to a joint, the guide defining an axis and having an outer contour formed to substantially conform to a portion of the joint. The first reference is attached at a fixed position relative to the joint. A positioning system is used to determine a position of the axis relative to the first reference, where the position of the axis is determined based upon the position of the guide while the guide is coupled to the joint. The guide is removed from the joint, and after the guide is removed from the joint, an instrument is positioned relative to the axis based on a position of a second reference relative to the first reference.
