We previously reported on the sporadic contamination by Legionella anisa of shower units and sink taps at Ryukyu University Hospital. Starting in July 2003, the neonatal area underwent an 8-month reconstruction, and in March 2005, the boiler system was replaced. We therefore examined shower water and tap water for the presence of Legionella just after replacement of the boiler system. In 3 of the 8 water samples collected from the remodeled area, we isolated Legionella pneumophila serogroup 1 and L. anisa. Moreover, L. pneumophila serogroup 1 was isolated in 4 of the 5 water samples gathered from the unreconstructed area of the same floor. Random amplified polymorphic DNA analysis suggested that a single clone of L. pneumophila might exist throughout the floors of the water distribution system. We replaced the shower units at the Legionella-positive site, and began flushing the sink-faucets with water heated to 55N for at least 1 h every morning. As a result, Legionella was not subsequently isolated in water samples. In this prospective study, we identified a central contamination by L. pneumophila serogroup 1 and showed that flushing with hot tap water was effective to counter this situation.