Vaporized hydrogen peroxide (VHP) is used to decontaminate clinical, biocontainment, and research animal rooms and equipment. To assist with its implementation in a murine facility, we developed a safe and effective method of VHP sterilization of IVC racks and air handling units (AHU). Safety of VHP decontamination was assessed by ensuring VHP levels dissipated to less than 1 ppm in the room prior to personnel reentry and inside the primary enclosure prior to the return of mice; this condition occurred at least 18 h after the VHP cycle. Efficacy of VHP sterilization was assessed by using chemical indicators, biologic indicators, and PCR testing for Staphylococcus xylosus, a commensal organism of murine skin and an opportunistic pathogen, which was present in 160 of 172 (93%) of specimens from occupied IVC racks and the interior surfaces of in-use AHU. Neither mechanized washing nor hand-sanitizing eradicated S. xylosus from equipment airway interiors, with 17% to 24% of specimens remaining PCR-positive for S. xylosus. 'Static-open' VHP exposure of sanitized equipment did not ensure its sterilization. In contrast, 'active-closed' VHP exposure, in which IVC racks were assembled, sealed, and connected to AHU set to the VHP cycle, increased the proportion of chemical indicators that detected sterilizing levels of VHP inside the assembled equipment, and significantly decreased PCR-detectable S. xylosus inside the equipment. Supplementing bulk steam sterilization of the primary enclosure with VHP sterilization of the secondary housing equipment during room change-outs may help to mitigate opportunistic agents that jeopardize studies involving immunodeficient strains.