Abstract: OBJECTIVE To investigate the current situation of disinfection effect in primary medical institutions of Qujing, so as to provide the basis for health administrative department. METHODS The environmental hygiene in primary medical institutions of Qujing from Mar. 2015 to Jul. 2015 were on-site sampled and tested, including ambient air, article surface, hand of medical staff, medical items, in-used disinfectant and dialysis water. The data were analyzed by SPSS 17.0. RESULTS The qualification rate of 259 medical institutions was 73.36%, and the qualification rate of samples of ambient air, article surface, hand of medical staff, in-used disinfectant and dialysis water had significant differences. The qualification rate of tertiary hospital was the highest among all medical Institutions, the qualification rate of the class-Ⅱ hospital was higher than the class-Ⅰ hospital, and the qualification rate of village clinics was the lowest. CONCLUSION The disinfection effect of grassroots medical institutions in Qujing is unoptimistic. Therefore, it is imperative to improve the supervision on grassroots medical institutions, especially the village clinics.