This paper deals with the vibration analysis of adjacent structures controlled by a magnetorheological (MR) damper and with the discussion of a numerical procedure for identification and definition of a reliable finite element model. The paper describes an extensive experimental campaign investigating the dynamic response, through shaking table tests, of a tridimensional four-story structure and a two-story structure connected by an MR device. Several base excitations and intensity levels are considered. The structures were tested in nonconnected and connected configuration, with the MR damper operating in passive or semiactive mode. Moreover, the paper illustrates a procedure for the structural identification and the definition of a reliable numerical model valid for adjacent structures connected by MR dampers. The procedure is applied in the original nonconnected configuration, which represents a linear system, and then in the connected configuration, which represents a nonlinear system due to the MR damper. In the end, the updated finite element model is reliable and suitable for all the considered configurations and the mass, damping, and stiffness matrices are derived. The experimental and numerical responses are compared and the results confirm the effectiveness of the identification procedure and the validation of the finite element model.