A system for the extraction, collection, processing and transplantation of cell subsets, including adult stem cells and platelets, in particular for tissue repair in regenerative medicine, comprises a set of disposable fluid- transport elements that are pre-connected or that include aseptic connectors for making interconnections between them in an aseptic manner or are adapted to be aseptically connected. The set usually includes three kits of disposable sterile elements, a collection kit, a processing kit, and a transplantation kit packaged in a blister pack on a support such as a tray, having one compartment for receiving each inter-connectable kit of the set. The set includes an extracting device, for example including a needle for bone puncture or vein puncture, for extracting bone marrow or other sources of cell subsets from a patient. The set also includes a collection chamber pre-connected or connectable to the extracting device, a processing chamber adapted to cooperate with processing equipment to perform processing and transfer operations on the harvested cells, and a reinfusion chamber for storing processed cells to be delivered back to the patient. The collection, processing and reinfusion chambers can be separate and pre-connected or interconnectable, or a multi-purpose processing chamber provides the combined functions of a collection-processing chamber, a processing-reinfusion chamber or a collection-processing-reinfusion chamber. The set also includes a transplantation device pre-connected or connectable to the reinfusion chamber for delivering processed cell subsets back to the patient. The whole process can be performed at the patient"s bedside, and is therefore considered as an on-line process.