Objectives: To test the efficacy of an intermittent use, dental unit waterline cleaner, containing 0.12% chlorhexidine, in a proprietary formulation, to reduce bacterial levels in three functioning dental units with independent water reservoir systems. Method and materials: Baseline water samples were first taken from six units. Two ounces of the undiluted test product was run through lines, left overnight, and flushed out the next morning. This was repeated for 6 nights initially, and once a week thereafter for 12 weeks. Three control dental units did not have chemicals added. Weekly samples were collected in bottles containing sodium thiosulphate on the afternoon before overnight treatment, plated on R2A agar, and incubated at room temperature for 7 days. Results: Mean colony-forming units per millimeter (CFU/mL) in treatment units declined from 23,389 (± 20,085) at baseline, to 6 (± 10) in week 4, to 5 (± 2) in week 12. Statistical analysis showed a significant difference between treatment and control units. Conclusion: Intermittent treatment of dental unit waterlines with 0.12% chlorhexidine gluconate (CHX), in a proprietary formulation, resulted in significantly reduced bacterial counts to levels that were consistently below the American Dental Association's goal of 200 CFU/mL for 8 weeks.