The theory of variational integration provides a systematic procedure to discretize the equations of motion of a mechanical system, preserving key properties of the continuous time flow. The discrete-time model obtained by variational integration theory inherits structural conditions which in general are not guaranteed under general discretization procedures. We discuss a simple class of variational integrators for linear second order mechanical systems and propose a constrained identification technique which employs simple linear transformation formulas to recover the continuous time parameters of the system from the discrete-time identified model. We test this approach on a simulated eight degrees of freedom system and show that the new procedure leads to an accurate identification of the continuous-time parameters of second-order mechanical systems starting from discrete measured data. (C) 2013 Elsevier Ltd. All rights reserved.