A method and system for assembling sets of medical instruments and/or pharmaceutical products. The system includes a control system comprising or being connected to a database comprising data objects corresponding to available objects. An input area is provided to receive batches of unsorted medical instruments or pharmaceutical product containers, and an identification area having an identification unit. A temporary sorting area is also provided, including a plurality of storage positions provided with visual indications capable of visually indicating one of the storage position at a time, and an output area, possibly being overlapping with the input area, arranged to receive medical instruments and/or pharmaceutical products as assembled sets. The controller is arranged to receive information from the identification unit obtained when an item is arranged on the identification area, and to identify the item in the database.