We all respond differently to drugs. Personalised medicine aims to improve efficacy and reduce side effects, and efforts are being made to understand the physiological differences that underlie responses to drugs. Genetics, diet and disease state can be key; however, gender also plays an important role in pharmacokinetics, pharmacodynamics and drug toxicity. Differences in metabolism and clearance of drugs as a consequence of distinct hepatic and renal processes in males and females are now much better understood but little is known about gender differences in the gastrointestinal tract. As the recipient of all orally administered medications, differences at this level can have a major impact on drug delivery and bioavailability; yet these continue to be ignored and insufficiently studied in the context of drug disposition. The aim of this review is to highlight the known gender differences in gut physiology. Clinical case studies are presented, where possible, to illustrate the influence of these differences on drug disposition and gaps in current knowledge are highlighted to encourage further research in this area.