EMPAT is an automated sampling system for research, product development, and commercial-scale biopharmaceutical manufacturing. EMPAT continuously samples products in-process, facilitating the testing protocols used for risk assessment and process validation. Through a menu of preauthorized and programmable sampling procedures, the system automatically collects samples for transfer to gamma-irradiated, single-use bag sets. Operating and batch data are captured, stored, and archived in an SQL database, with capabilities for report generation and barcode label printout for sample identification.