System identification based on the black box models was utilized for understanding of the transfer function of the foot and ankle exposed to vertical excitation. Various linear polynomial structures and state-space model were tested by comparing the measured acceleration at the base, the Medial Malleolus, and the Tibial Tuberosity respectively for input and output. Identified models are well matched with the measured data when the high model order was selected. The Output Error model has generally shown the best fit to the data, while in several cases the state-space model presents better fit. These results can be used as a starting point for the nonlinear black box model and the grey box model.