This paper presents a response spectrum analysis procedure suitable for base isolated regular buildings subjected to near fault ground motions. This procedure is based on the fact that the isolation system may be treated separately since the superstructure behaves as a rigid body on well selected isolation systems. The base isolated building is decomposed into several single-degree of freedom systems, the first one having the total weight of the building is isolated while the remainder when superposed they replicate approximately the behavior of the superstructure. The response of the isolation system is governed by a response spectrum generated for a single isolated mass. The concept of the procedure and its application for the analysis of base isolated structures is illustrated with an example. The present analysis procedure is shown to be accurate enough for the preliminary design and overcomes the limits of applicability of the conventional linear response spectrum analysis.