Abstract: Objective To learn medical waste management status of pathogenic microorganism laboratories in Putuo District, and provide evidence for laboratory medical waste and laboratory biosafety management.Methods 57 laboratories which generate medical waste were investigated and analyzed through questionnaire and on-site supervision and inspection.Results There were differences in the medical waste management system in units with different nature and levels of the laboratories. Medical waste disposal facilities in the laboratory of non-medical and health units were deficient. Centralized disposal capacity of medical waste could not meet the demands of small medical institutions and non-medical health units.Conclusion The management of the weak link for the pathogenic microorganism laboratories needs to be strengthened; the medical waste management system needs to be improved; new work concept of pre-trial in laboratory construction needs to be introduced; and contradictions between medical waste disposal demand and disposal capacity needs to be resolved. It is also suggested that laboratories should be under classified administration according to the different nature of their affiliated institutions.