Ensuring the safety of therapeutic modalities produced and purified from biological systems is of high concern. Regulatory authorities and the biopharmaceutical industry are continuously seeking to improve methods for the detection, identification, inactivation and removal of potentially contaminating pathogens in biotherapeutic products. Current methods for pathogen detection and identification are designed to discover adventitious as well as known microbial species in product samples. Many of these approaches require weeks or even months of observation, and the time involved is often a constraint on product release. This review focuses on current practices and technologies that have emerged in recent years, and highlights advances that have accelerated the time required for, and accuracy of, pathogen detection and identification. The biopharmaceutical industry has employed a multifaceted approach in pathogen detection, including the rigorous screening of blood/plasma donations; documented sourcing and screening of raw materials; thorough testing of production cell substrates and cell culture harvest material during processing, and at the stage of a final purified drug substance; and the evaluation of microbe clearance during purification operations. All these practices strive to ensure safety and mitigate the risk to patients undergoing biotherapeutic treatment.