This paper deals with the dynamic tests carried out with the purpose of controlling the behavior of the recently built Caffaro Viaduct. This test was required to integrate the final load test in view of the importance of the viaduct and because of its structural typology that implies a particular and quite complex dynamic behavior. The structural control is performed by comparing modal parameters obtained experimentally with those predicted by the design structural model, and represents the first step of a future structural health monitoring program that foresees tests performed every two years. The Caffaro Viaduct is a part of the project for modernization and retrofit of the A3 highway (Salerno-Reggio Calabria), near Lauria in south Italy. The longitudinal development of the viaduct is about 400 m; it is formed by two separate steel-concrete composite decks, 12.7 m wide, supported each one by two steel trestles that are connected nearly the top by transverse steel truss beams. The overall dynamic response of the structure is checked by means of three different sensor placements with the aim to highlight three different behaviors: i) the global behavior of both carriageways, ii) the flexural-torsional behavior and iii) the transverse one of the southbound carriageway. The data collected during ambient vibration tests are processed with Stochastic Subspace Identification Covariance Driven in order to estimate the modal parameters. Natural frequencies and mode shapes experimentally determined are compared with the numerical ones obtained with the predictive finite element model developed for design purposes and then with the model slightly modified to account for the real operating conditions of the viaduct, in terms of both stiffness and masses. A refined model updating is in progress to fix a benchmark, necessary for the scheduled structural health monitoring program.