This study addresses the efficacy of an automated decontamination protocol using the germicide 'tetra acetyl ethylene diamine (TAED) perborate' (Farmec SpA, Italy). The germicide TAED perborate protocol is used in the Castellini Dental Units fitted with an Autosteril unit (an automated device that can cycle 0.26% TAED perborate solution and sterile water for cleaning the water system between patients and overnight). Prior to testing the Autosteril and the 0.26% TAED perborate protocol on the Logos Jr Dental Unit (Castellini SpA, Italy), TAED perborate was used on a dental unit water system simulation device. A dental unit water system simulation device equipped with four dental unit water systems and with naturally grown and mature biofilm contamination was used in this study (three treatment units and one control). One treatment group used a simulated 5 minutes contact with TAED perborate and sterile water for irrigation; the second used a simulated 5 minutes contact with TAED perborate and 2 ppm ClO2 for irrigation; the third used a simulated 5 minutes contact with TAED perborate and municipal water for irrigation. The control group used municipal water for irrigation with no cleaning/disinfection protocols. This protocol was repeated for 30 cycles. Laser scanning confocal microscopy (LSCM) was used to study the effects on natural and mature biofilms, and R2A agar used to quantify heterotrophic plate counts in the effluent irrigant. Antimicrobial efficacy was evaluated by challenging TAED perborate with microbes and spores (M. smegmatis and B. subtilis). Deleterious effects of the germicide were evaluated on metal and nonmetal parts of dental unit water systems. Heterotrophic plate counts using R2A agar and LSCM of the lines were conducted to assess biofilm and microbial control. Baseline water samples showed mean contamination >5.6 log10 cfu/ml. After initial cleaning, all three groups maintained mean contamination levels of less than 1.1 (SD <0.3) log10 cfu/ml. LSCM of baseline samples was positive for live biofilm in all groups. At the end of the study, viable biofilm was only present in the control. In the microbial challenge test, all vegetative organisms were killed within 30 seconds of contact, while spores were killed within 5 minutes. Corrosion was seen in metals used in US-manufactured dental unit materials, while not observed in those used in the Castellini Logos Jr dental unit. In this study, the TAED perborate protocol was effective in biofilm control and control of dental treatment water contamination. Use of sterile water or 2 ppm ClO2 along with TAED treatment also controlled planktonic contamination effectively. Environmental biofilms contaminate dental unit water systems over time and affect the quality of dental treatment water. Contaminants include environmental biofilms, microbes, including gram-negative rods and endotoxins in high doses that are not of acceptable quality for treating patients. There are many germicidal protocols for treating this contamination and one such is the prescribed use of TAED perborate used in conjunction with sterile water for irrigation in the autosteril device, an integral component of the Castellini dental units for between patient decontamination of dental unit water systems. This study was conducted on an automated simulation dental unit water system to test the TAED perborate protocol's efficacy on naturally grown, mature environmental biofilms, it's efficacy on microbes and spores and it's effects on materials used in dental unit water systems. This translational research addresses both microbial control and material effects of TAED perborate in studying efficacy and possible deleterious effects and simulated use in dentistry. Currently, this antimicrobial use protocol is followed worldwide in the Castellini dental units that are used in day-to-day dental patient care.