Legionella colonization in hospital hot water distribution networks was evaluated following 36 months of continuous treatment with monochloramine and compared with chlorine dioxide. Nitrite, nitrate, chlorite, chlorate, bromide, trihalomethanes and haloacetic acids as well as the biocide concentration at sampled points were measured. Only 8/84 samples treated with monochloramine were found contaminated and after the first 8 months of treatment no Legionella was isolated. Chlorine dioxide was associated with a strong reduction in Legionella contamination compared to pre-treatment, but differences according to the device were observed. Monochloramine between 2 and 3 mg l(-1) and chlorine dioxide between 0.50 and 0.70 mg l(-1) were needed to control Legionella colonization. Comparing no- and post-flush samples, a higher frequency of no-flush positive samples was noted using chlorine dioxide, suggesting an increased risk for patients when they open the tap. No increase in chlorite levels and no water nitrification occurred by using monochloramine. Chlorite at levels exceeding the limit requested for drinking water was measured when chlorine dioxide was applied. In conclusion, we highlight that continuous injection of monochloramine should be considered as an effective alternative to chlorine dioxide in controlling legionellae contamination inside hospital water distribution systems.