Complex modal analysis and a two-stage system identification technique is employed for investigating the effect of structural details on seismic performance of four multispan, continuous base-isolated bridges in Japan from recorded seismographs. Comparison of system identified and experimental values of stiffness and damping revealed that the behaviour of the bridges is significantly altered by structural/non-structural details like metallic bearings, side stoppers and bearing keeper plates. Friction in metallic bearings, which are used at the end spans of two bridges, is found to be the major cause for substantial increase in stiffness and damping of super-structure of these bridges. This effect is found to diminish with increasing seismic amplitude. A similar phenomenon is found to be present in the transverse side-stopper of the third bridge. On the other hand, bearing keeper plates got locked with girders and prevented base-isolation from performing its intended function in the fourth bridge. Further investigation in conjunction with rigorous modelling of the pile-supported sub-structure revealed that locking of base-isolation bearings at one pier resulted in substantial unequal lateral load distribution to the substructure. This study thus signifies the attention that should be devoted to such details for desired functioning of these pioneering structures.