The United Nations named 2010 as a year of natural disasters, and launched a worldwide campaign to improve the safety of schools and hospitals from natural disasters. In the region of South East Europe, Croatia and Serbia have suffered the greatest impacts of natural disasters on their communities and health facilities. In this paper the disaster management approaches of the two countries are compared, with a special emphasis on the existing technological and legislative systems for safety and protection of health facilities and people. Strategic measures that should be taken in future to provide better safety for health facilities and populations, based on the best practices and positive experiences in other countries are recommended. Due to the expected consequences of global climate change in the region and the increased different environmental risks both countries need to refine their disaster preparedness strategies. Also, in the South East Europe, the effects of a natural disaster are amplified in the health sector due to its critical medical infrastructure. Therefore, the principles of environmental security should be implemented in public health policies in the described region, along with principles of disaster management through regional collaborations.