An automated system and method for processing vessels containing biological samples are presented. The system comprises vessel holders, a transport medium for transporting the vessel holders between the components of the system, a work cell for processing, a storage module for empty vessel holders, wherein the storage module is connected to the transport medium, a robotic manipulator for engaging and/or disengaging the vessels with empty vessel holders, an empty vessel holder transfer unit for introducing empty vessel holders into or retrieving them from the storage module, and an empty vessel holder detection unit, including an empty vessel holder detector for discriminating between filled and empty vessel holders as well as a transfer initiator configured to initiate the introduction or re-introduction of an empty vessel holder detected in or on the transport medium into the storage module by the empty vessel holder transfer unit.