Natural disasters result in impacts on the population's health, damage to healthcare establishments, and, in extreme situations, the health systems' breakdown. National and global trends show an increase in the frequency of disasters associated with climate change. This article aims to analyze the impacts and economic costs of natural disasters for healthcare establishments, identifying the most frequent and costly types and distribution across the Brazilian territory, based on data recorded in Brazil's Integrated Disaster Information System (S2ID) from 2000 to 2015. A total of 15,950 records were systematized and analyzed, of which only 29.4% of the events showed records of costs, totaling nearly BRL 4 billion. Climate disasters were the most frequent, but they did not account for the highest costs. In the cost per event ratio, the costs of hydrological disasters were 3.2 to 3.6 higher than for climate and geologic disasters. Pernambuco, Amazonas, and Santa Catarina were the states with highest total costs in millions of Brazilian reais. The North region, especially the state of Acre, had the highest cost per disaster. Despite the study's limitations (involving the records' quality), the data should be viewed as the tip of an iceberg, since the impacts go beyond the economic damages, impacting the infrastructure and resources that support services, compromising their capacity precisely when the population most needs health services.