The selection of an appropriate and/or standardized method for representing 3-D joint attitude and motion is a topic of popular debate in the field of biomechanics. The joint coordinate system (JCS) is one method that has seen considerable use in the literature. The JCS consists of an axis fixed in the proximal segment, an axis fixed in the distal segment, and a "floating" axis. There has not been general agreement in the literature on how to select the body fixed axes of the JCS. The purpose of this paper is to propose a single definition of the body fixed axes of the JCS. The two most commonly used sets of body fixed axes are compared and the differences between them quantified. These differences are shown to be relevant in terms of practical applications of the JCS. Argumentation is provided to support a proposal for a standardized selection of body fixed axes of the JCS consisting of the axis ê1 embedded in the proximal segment and chosen to represent flexion-extension, the "floating" axis ê2 chosen to represent ad-abduction, and the axis ê3 embedded in the distal segment and chosen to represent axial rotation of that segment. The algorithms for the JCS are then documented using generalized terminology.