Legionnaires’ disease is an established and frequent cause of hospital-acquired pneumonia in adults. However, it can also affect children, particularly with immunodeficiencies. Hot water supply systems and any equipmen generating water-air aerosol are the main sources of Legionella infection in healthcare facilities. The aim of our study was to determine the frequency of Legionella colonization of water supply systems in children’s wards in hospitals. In 5 hospitals water samples were collected from water network (29 samples), air conditioning device (1 sample) and from medical ventilator (1 sample). The samples were examined using the NIPH-NIH membrane filtration method and PN-ISO 11731-2:2006 method. Legionella was isolated from water samples taken in 3 of 5 hospitals (60% of studied healthcare facilities), in 25 water samples (80% of tested samples). Among 353 isolated strains, 230 were identified as L. pneumophila sg 2-14. The most hazardous L. pneumophila sg 1 was not isolated. In 74% of positive samples the number of bacteria exceeded 100 cfu in 100 ml. The results of our study indicate relatively high frequency of Legionella colonization of water systems in children’s wards in hospitals. In order to reduce/minimize the health risk, measures to prevent Legionella colonization in healthcare facilities are necessary, including the proper design of water system and its maintenance in accordance with appropriate standards. There is also the necessity to sample hospital water routinely to detect Legionella and prevent the outbreaks, not only from water supply systems, but also air conditioning systems and medical equipment.