Legionnaires' disease is a known cause of severe pneumonia in a nosocomial setting. This study examined Legionella isolation in Greek hospitals. Water samples and swabs of showerheads from 41 hospitals were collected over a four-year period (2004-2007) from hot and cold water systems and cooling towers in Greece. In total, 1058 samples were examined for the presence of Legionella. From the hot water samples examined, 166 out of 607 (27.3%) were positive for Legionella, including 111 (18.3%) positive for Legionella pneumophila sg1 samples. The temperature of hot water samples less than 55°C was statistically significant, associated with Legionella spp. isolation (RR 4.01, 95%CI 2.33-6.92). Ten out of 17 (58.8%) hospital cooling towers required remedial actions due to Legionella colonization. Reemergence of Legionella spp. colonization was evident in more than half of the hospitals where frequent monitoring and appropriate risk assessment plans were absent or lacking. Hospitals that were monitored continuously over the study period presented a decreasing trend of Legionella colonization. Environmental risk assessment together with Legionella isolation should be enforced systematically in hospitals.