At present, intermodal logistics centers play an important role in the world in context of transport and logistics services. The purpose of this paper is to propose the methodology for selecting the appropriate storage area design for intermodal transport units (ITU ́s) in intermodal logistics center. In this matter, four different scenarios of storage area design were taken into. Storage area configuration can significantly influence the logistics and transport services productivity and can have a significant impact on the economics effectiveness of the enterprise. In the paper, the AHP method is used in the context of selecting the appropriate design. This method is able to assess each design in regard to each of the determined criterion and finally prioritize all the designs.