Objective To provide the basic data to effectively implement and evaluate the National Malaria Elimination program and projects funded by the Global Malaria Fund by ascertaining the prevalence of malaria and capacity for malaria prevention and control. Methods A baseline study was conducted in accordance with national guidelines and study sites were selected by stratified random disproportionate sampling based on the prevalence of malaria. Results A total of 3 163 malaria cases were reported in Yunnan Provi...