A method for reconciliation in a drug filling line includes providing a batch number relating to a predetermined batch of containers to be filled with a drug. Each one of the containers is marked with a unique identifier differentiating and/or identifying each container among others. Each unique identifier is stored and associated with the batch number by a processing and control unit, before starting the filling step of each container. Filled containers are flashed by at least one identifier reader to check correspondence between the batch number being processed and each filled container, in order to validate or reject in real time each container with respect to a predetermined batch being processed by the filling line.