Monitoring of hospital water systems to prevent and control nosocomial legionellosis is important from a public health perspective. This study was conducted to survey the prevalence of Legionella contamination of hospital waters. A total of 44 water samples from the hot-water system of 11 hospitals were tested for Legionella by a culture method and a nested polymerase chain reaction (PCR) assay with Legionella-specific primers to identify the more sensitive method. Some physicochemical parameters and heterotrophic plate counts of water samples for possible association with Legionella contamination were also determined. The contamination rate of hospitals in our study varied between 64% (eight of 11)–100% based on culture method and nested PCR, respectively. Of the 44 water samples examined, 23% were positive for Legionella spp. by the culture method, while the nested PCR assay using the primers LEG448-JRP revealed 66% of the water samples being positive. Given the importance of monitoring hospital water systems for the presence of Legionella spp., the present PCR assay proved highly applicable for practical and sensitive surveillance of Legionella in such water systems. In addition, rapid monitoring of Legionella contamination could eliminate the potential exposure of high-risk patients through effective control measures.