Functional gastrointestinal disorders, including irritable bowel syndrome and functional dyspepsia, are highly prevalent disorders affecting approximately one in four people in Western societies. This article reviews examples of the role of pharmacogenomics in the safety and efficacy of medications used in the management of such disorders. These include variations in the effects of medications metabolized by cytochrome P450 enzymes (e.g., 2D6 and 2C19), and the effects of genetic polymorphisms in the promoter of the serotonin transporter protein, which influence the response to alosetron in patients with diarrhea-predominant irritable bowel syndrome. These observations suggest that pharmacogenomics will introduce a new era in pharmacotherapeutics in gastroenterology.