In this work, seismic risk assessment of hospitals in Lima city is presented. The aim of this paper is to evaluate the seismic risk of the Lima’s health system at Metropolitan scale. Seismic Risk Analysis has been carried out utilizing the Comprehensive Approach for Probabilistic Risk Assessment methodology (CAPRA). Geographic Information System (GIS) tools have been used to model the risk components: hazard, exposure and vulnerability. A total of 41 hospitals have been evaluated in order to obtain risk indicators in terms of economic losses. The results show that after an 8.2 magnitude earthquake with an epicenter in the coast of Lima, 85% of hospital buildings have more than 10% of structural damage. Furthermore, the expected annual loss (EAL) is 2% of the replacement value, which is high and uncompetitive compared with the values of the insurance sector market. This study seeks to understand and evaluate the hospitals seismic risk at metropolitan level in order to define measures, priorities and actions for the future development of Lima’s health system.