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The antimicrobial thermoplastic starch (ATPS) containing guanidine-based polymers was obtained using a twin-screw extrusion with potato starch and polyhexamethylene guanidine hydrochloride (PHGH). Furthermore, the non-leaching antimicrobial biodegradable poly(butylene adipate-co-terephthalate) (PBAT) was prepared through reactive extrusion with PBAT and ATPS in the presence of the coupling agent, 2,2'-(1,3-phenylene)-bis (2-oxazoline) (PBO). Finally, the antimicrobial PBAT films were obtained by using a blown film extrusion system. The mechanical properties of the antimicrobial PBAT films varied with the contents of ATPS and thermoplastic starch (TPS). According to the test results of shaking flask method, the prepared antimicrobial PBAT films showed excellent antimicrobial activities (antimicrobial rate >99.99%) and rapid pathogen deactivation efficiency (antimicrobial rate >99.99% even within 15s of contact time). The water washing and ring diffusion tests demonstrated that the antimicrobial film was a non-leaching product. Inspiringly, the antimicrobial PBAT films with an excellent antimicrobial activity can be obtained even at a very low dosage of PHGH (1.0 mg/g PBAT film)., (Copyright © 2015 Elsevier B.V. All rights reserved.)