Objective To verify the technics of inactivating/removing pathogens in medical chitosan derived from shrimp shell. Methods Possible pathogen species were included according to the raw material of shrimp shell used in production, then bacillus cereus, porcine parvovirus (PPV) and pseudorabies virus (PRV) were selected as indicator pathogens.Pathogen solution was prepared in accordance with Technical Standard for Disinfection. The processing procedure of medical chitosan was analyzed to determine whether the alkal ization of chitin and the filter steril ization of chitosan were capable of inactivating/removing pathogens and their efficiencies were tested. Results Bacillus cereus was removed by 8 184 cfu/ mL after alkal ization and 30 818 cfu/mL after filter steril ization. The average logarithm inactivation value (LIV) of PPV and PRV after alkal ization were equal to or above 4.76 logTCID50/0.1 mL and 6.67 logTCID50/0.1 mL, respectively, and their average LIV after filter steril ization were 2.25 logTCID50/0.1 mL and 3.04 logTCID50/0.1 mL. The alkal ization of chitin inactivated/removed indicator pathogens effectively, while the filter steril ization of chitosan removed bacterial effectually but could not inactivate viruses completely. Conclusion The alkal ization of chitin can be used as the technics of inactivating/removing pathogens during the preparation process of medical chitosan to guarantee the safety of the product.