Water from the dental unit waterlines (DUWLs) is known to contaminate with microbial from the biofilm that formed in the tubing system. The water quality from DUWLs is important to patients and dental health care professionals as they could be infected either directly from the contaminated water or aerosol that is generated during dental procedures. Suppliers claimed that dental units supplied to the hospital can only use a specific disinfectant which is uneconomic compared with the others. The aims of this study were to evaluate and compare the efficacy of different disinfectant on the water quality of DUWLs. Four disinfectants (Calbenium, A-dec ICX tablet, Dentel 5, Metassys) and distil water were evaluated. 350 mL water sample was collected separately, from the outlet of high-speed handpiece, scaler, 3-ways syringe and cup filler into a sterile thiosulfate bag on the 1st, 2nd, 4th, 8th, 12th and 24th weeks of the study. The samples were tested on the following day for total viable count (TVC). There is significant difference in the efficacies of the different disinfectants. Only one disinfectant consistently produces water quality within the recommended level of American Dental Association (ADA). Within the limitation of this study, it was found that there is alternative disinfectant that can reduce the TVC to the level recommended by ADA. However, the water qualities produced with these disinfectants were not consistent although they did not cause any technical problem to the dental units during the period of study.