The objective of the study was to develop a framework for the accurate identification of joint centers to be used for the calculation of human body kinematics and kinetics. The present work introduces a method for the functional identification of joint centers using markerless motion capture (MMC). The MMC system used 8 color VGA cameras. An automatic segmentation-registration algorithm was developed to identify the optimal joint center in a least-square sense. The method was applied to the hip joint center with a validation study conducted in a virtual environment. The results had an accuracy (6mm mean absolute error) below the current MMC system resolution (1cm voxel resolution). Direct experimental comparison with marker-based methods was carried out showing mean absolute deviations over the three anatomical directions of 11.9 and 15.3mm if compared with either a full leg or only thigh markers protocol, respectively. Those experimental results were presented only in terms of deviations between the two systems (marker-based and markerless) as no real gold standard was available. The methods presented in this paper provide an important enabling step towards the biomechanical and clinical applications of markerless motion capture.