Staphylococcus aureus, a leading cause of serious human infections in both healthcare and community settings, is increasingly difficult to control due to expanding resistance to multiple antibiotic classes. Methicillin-resistant S. aureus (MRSA) strains have disseminated on a global scale and are associated with adverse patient outcomes, increased hospital stays, and significant economic costs to the healthcare system. A proximal step in S. aureus infection is colonization of the nasal mucosa, and effective strategies to decolonize high risk patients to reduce the risk of invasive infection and nosocomial spread represent an important clinical priority. With rising resistance to mupirocin, the most common antibiotic utilized for nasal MRSA decontamination, we are examining the use of pure molecular iodine (I2)-based formulations for this indication. Recently, an iodophor formulation of povidone-iodine (PVP-I) has shown significant promise for nasal MRSA decontamination by swabbing the anterior nares of patients in hospital settings, but the I2 concentration in this treatment is less than 0.01% of total iodine species present and like all providone-iodine formulations causes skin staining. Here we determine that a novel non-staining formulation of I2 combined with the safe organic emollient glycerin delivers high local concentrations of the active antimicrobial entity (I2) with minimal evaporative loss, exhibits activity at ∼1 part per million against MRSA and other important Gram-positive and -negative human pathogens. This formulation for I2 topical delivery produced similar reductions in mean bacterial burden and was associated with fewer treatment failures (<2-logfold reduction) than PVP-I in a murine model of MRSA nasal decontamination. Formulations of I2 in glycerin emollient merit further exploration as topical disinfectants for human medical indications.