Aerobic bacterial culture was used to compare the effectiveness of the current USDA footwear disinfection protocol for airplane passengers contacting livestock to a novel protocol. The current protocol consists of brushing and dipping shoe soles in 1% Virkon S. The number of bacteria was not different between shoes treated with the current protocol and untreated shoes. No shoes met the standard for disinfection after the current disinfection protocol was completed. The novel protocol consisted of brushing shoe soles, wiping soles with a cotton towel soaked in 1% Virkon S, and drying soles with paper towels. The number of bacteria was less (P<0.0001) on treated shoes compared to control shoes. Eighteen of 20 shoes (90%) cleaned using the novel protocol met the standard for disinfection. Direct comparison of the current and novel protocols found that the number of bacteria cultured was less (P<0.0001) after implementing the novel protocol compared to implementing the current protocol. Again, no shoes treated using the current protocol met the standard for disinfection after the current protocol was completed. Sixteen and 17 of 20 shoes (80--85%), respectively, met the standard for disinfection after the novel protocol was completed. Under conditions of this study, current US airport footwear disinfection protocols were inadequate to disinfect footwear when using aerobic bacteria as a marker for disinfection. We recommend implementation of the novel footwear disinfectant protocol for select passengers from international flights.