OBJECTIVE： To investigate the current situation and reasons of drug shortage in medical institutions of Yunnan province， and to provide reference for solving the drug shortage. METHODS： A questionnaire survey was conducted to investigate and analyze the situation of drug shortage in 61 medical institutions from Yunnan province （19 third-level hospitals， 26 second-level hospitals， 16 first-level hospitals）. By SPSS 19.0 software， descriptive statistics was used to stratify， summarize and analyze the data of different levels of hospitals. RESULTS： A total of 61 questionnaires were sent out， and 57 effective ones were collected with effective recovery of 93.44％. From the distribution of drug shortage， the overall proportion of first-aid drug in third-level hospitals was 22.73％， which was higher than those of second-level and first-level hospitals； among all types of National Essential Medicine List and Yunnan Province Medical Insurance Medicine List， the overall proportions of shortage drugs in first-level hospitals both were 97.58％， higher than third-level and second-level hospitals. From the types of shortage drug， the proportion of anti-infective drug shortage ranked the top two places in different levels of hospitals， and those of Chinese patent medicine preparation shortage ranked the first place in second-level and first-level hospitals. The reasons of drug shortage were all related to pharmaceutical production enterprises， distribution enterprises and medical institutions. Drug shortage of third-level and second-level hospitals mainly manifested as out of stock in distribution enterprises. Drug shortage of first-level hospitals mainly manifested as no drug supply and price inversion in bidding platform. CONCLUSIONS： The situation of drug shortage is still grim in Yunnan province. The reasons for drug shortage are correlated with drug production， distribution and application. It is urgent for us to establish a long-term mechanism for drug shortage prevention and disposal in order to prevent drug shortage effectively and to ensure that patients can continue to obtain safe and effective drugs.