Abstract: Three years after the great earthquake in May 2006, Bantul succeeded in recovering in many sectors, including health. However, Bantul still faces many health problems that should be overcome with limited resources. Therefore, this research identifies, analyzes, and sets the priorities of health problems in order to provide recommendations for efficient and effective health policies and program planning in Bantul. This analysis is a descriptive observational research which analyzes secondary data from the Health Department of Bantul District. Health problem priority was set using the Hanlon method. In a series, the top ten priority health problems are Maternal mortality, HIV/AIDS, Infant mortality, Tuberculosis, Diabetes Mellitus, Dengue Haemorrhagic Fever, Hypertension, Malnutrition, mortality of children under five, and Diarrhea. Thereby, Bantul district still has a double burden. On the one hand, infectious diseases are still at a high rate. On the other hand, the degenerative disease also continues to increase and reach a large number of sufferers.