This work studies the influence of a vibration isolator on the response of a flexible base structure. Two strategies are compared: passive and active vibration isolation (PVI, AVI). Although the multiple advantages of AVI over PVI techniques are well known, their effect in the base structure has not to date been compared. This interaction has an important role in the performance of the general control system, especially when the vibration isolation system is not the only system on the base structure or when there are multiple isolators working simultaneously on it. In addition, the structural serviceability of the base structure can also be affected. The analysis of the vibration isolation problem is made from a wide perspective, including the effect that isolator has on the base structure. Hence assuming the base structure is a non-rigid system. The effect of the isolation system on the base response is studied for an extensive range of base structures, thus showing different possible scenarios. The influence is quantified by comparing the peak magnitude response of the base when both passive and active vibration isolation techniques are used. The theoretical results have been corroborated by undertaking experimental tests on a full-scale laboratory structure.