The stewardship of antimicrobial use in livestock production systems is widely viewed as an important element in a multi-faceted approach to reduce the potential emergence of antimicrobial resistant populations of bacteria that could present a public health risk. In this study, we compare the impact of five commonly used antimicrobials on the resident microflora of the porcine upper respiratory tract. In view of the importance of respiratory disease in pig production, understanding these changes could be a critical step in designing comprehensive health management programs that optimize local immunity to respiratory infections and potentially reduce the need for antibiotics.