3D calibration was performed for a GPR measurement system for concrete bridge decks. An old bridge having been repaired approximately two years prior with a new bridge deck part was considered in the test results. The deck, including then visible subsurface features, was measured earlier during the construction phase using a 3D laser scanning system, then after construction by two different GPR measurement systems and antennas. Several subsurface structural layers as well as the deck reinforcement were measured by the GPR systems. These 3D point clouds were compared with the mid-construction laser scanned point clouds. The results showed high accuracy in measurements of reinforcement, but less accuracy in measurement of concrete surface under road layers. Future development possibilities are also discussed.