This paper proposes a new protocol designed to track a large number of foot segments during the stance phase of gait with the smallest possible number of markers, with particular clinical focus on coronal plane alignment of the rear-foot, transverse and sagittal plane alignment of the metatarsal bones, and changes at the medial longitudinal arch. The shank, calcaneus, mid-foot and metatarsus were assumed to be 3D rigid bodies. The longitudinal axis of the first, second and fifth metatarsal bones and the proximal phalanx of the hallux were also tracked independently. Skin markers were mounted on bony prominences or joint lines, avoiding the course of main tendons. Trajectories of the 14 markers were collected by an eight-camera motion capture system at 100 Hz on a population of 10 young volunteers. Three-dimensional joint rotations and planar angles were calculated according to anatomically based reference frames. The marker set was well visible throughout the stance phase of gait, even in a camera configuration typical of gait analysis of the full body. The time-histories of the joint rotations and planar angles were well repeatable among subjects and consistent with clinical and biomechanical knowledge. Several dynamic measurements were originally taken, such as elevation/drop of the medial longitudinal arch and of three metatarsal bones, rear-foot to fore-foot rotation and transverse plane deformation of the metatarsus. The information obtained from this protocol, consistent with previous clinical knowledge, enhanced our understanding of the dynamics of the human foot during stance.