In this paper, identification of energy dissipation in the joints of a lab-scale structure is accomplished. The identification is carried out by means of an energy flow analysis and experimental data. The devised procedure enables to formulate an energy balance in the vicinity of the joints to obtain local energy dissipation. In this paper, a damping matrix based on the locally identified damping coefficients is formulated. The formulated damping matrix is later used in a five-degrees-of-freedom (5DOF) system for validation. The results obtained with the proposed method are in good agreement with the experimental data, especially in the low frequency range.