An apparatus and method for the batch photoactivation of mononuclear cells (MNCs) is described. The system includes a programmable controller configured to automatically separate whole blood in a first collection cycle to obtain a first quantity of MNCs； separate whole blood in a second collection cycle to obtain a second quantity of MNCs while simultaneously photoactivating the first quantity of MNCs to obtain a first quantity of treated MNCs； either store the first quantity of treated MNCs or reinfuse the first quantity of treated MNCs； photoactivate the second quantity of MNCs to obtain a second quantity of treated MNCs； either store the second quantity of treated MNCs or reinfuse the second quantity of treated MNCs； and reinfuse any blood components remaining after the second collection cycle.
