In vivo microdialysis (MD) is an innovative clinical technique that has been employed in preclinical research and metabolic studies in patients for more than a decade. Recently, MD has been adopted for human drug studies and has opened up the opportunity to quantify tissue drug distribution in vivo. The particular advantage of MD for the anti-infective field relates to the fact that MD allows for online measurement of the unbound, pharmacologically active drug fraction in the interstitial space fluid (ISF), the anatomically defined target site for most bacterial infections. The aim of this review is to provide an overview of the current literature about MD in anti-microbial drug studies. It will be shown that MD has become feasible in most human tissues including brain and lung. So far, several MD studies have demonstrated that anti-microbial concentrations at the effect site may be subinhibitory, although effective concentrations are attained in serum, a finding that has significant impact on clinical decision making. In addition to its property as a pharmacokinetic sampling technique, MD offers unique opportunities in pharmacokinetic-pharmacodynamic (PK-PD) research and has the potential to streamline the decision process on proper drug dosing in drug development.