In Anhui province, all primary medical institutions were selected in the pilot areas for comprehensive evaluation of infectious disease prevention and treatment in a medical institution in 2016,aimed to understand the current situation of medical waste management in primary medical institutions in Anhui province, and to provide reference for the supervision of medical waste in primary medical institutions. A total of 634 primary medical institutions were supervised. Of which 139 institutions were classified as excellent （21.92%）, 354 as qualified（55.84%）, and 141 as key supervision（22.24%）. There was significant difference of the classified proportion among primary medical institutions in northern area, central area and southern area of Anhui province（P<0.05）. The completion proportions according law and regulation of medical waste collection package and seal, temporary storage equipment and its disinfection, sewage treatment contaminated by infectious disease pathogens, management personnel’s occupational safety protection were lower than 60%. The current situation of medical waste management in primary medical institutions in Anhui province is not optimistic. The supervision and management of clinical waste should be strengthened, especially for the institutions in the northern province. The packaging and sealing of medical waste collection and the equipment for temporary storage of medical waste shall be the key contents of supervision.