The objective of the present study was to investigate reduction in the colonization and growth of heterotrophic bacteria in dental unit waterlines by using hydrogen peroxide/colloidal silver as disinfectant. Twenty-seven dental units were included; 6 units that were more than 20 years old and 7 units that had been in use for 2 years comprised the old and new treatment groups, respectively. Fourteen units served as controls. The treatment groups were disinfected continuously and every 4 weeks shock doses were applied over a 20-week period. Water samples were taken before treatment, 1 and 2 weeks after treatment, and thereafter every 4 weeks; then they were inoculated onto R2A agar plates. While 1-16-week results for the old treatment group showed total heterotrophic bacterial counts of higher than 1 x 10(5) cfu/mL, at 20 weeks they were below 7.5 x 10(2) cfu/mL. Only 2 units were able to reach levels of <= 200 cfu/mL, which is the dental unit water quality standard. For the new treatment group it was achieved for all units after 1 week. Electron microscopic analysis also revealed that while biofilm formation was more evident in the old treatment group, after a longer treatment period biofilms were eliminated completely. The findings indicate that disinfection was effective in improving the output water quality using hydrogen peroxide/colloidal silver disinfectant.