Antimicrobial therapy is an important part of wellness and general health. The advancement of antibiotic therapy must be tempered with the realization that drug resistance is increasing. This discussion will focus on reviewing the current antibiotic therapies available and how to use them in clinical practice based on a syndrome approach. The presentation will also focus on a non-drug approach to infection control. Recent advancement and information on re-colonization and restoring the normal flora of an individual after being on antimicrobial is gaining popularity in naturopathic medicine and allopathic medicine. The decrease in collateral damage (disruption of normal flora) can be reduced by understanding pharmacokinetic and pharmacodynamic principles of antimicrobial therapy, non-drug measures to restore normal flora and the concept of xenobiotic therapy. This review will outline the most common infectious disease syndromes, the most likely pathogens involved in disease manifestation, and the clinical intervention required to return an individual to their normal wellness.