Pharmacogenomics is the study of genetic variations that produce a modification of the response to drugs. These variations are expressed as a different capacity for the metabolism or the transport of drugs, or a variable activity of drug receptors. Drug use in gastroenterology offers different examples of the use of pharmacogenomic analysis in the identification of the appropriate drug and drug dose for each individual patient. The use of proton pump inhibitors in the treatment of gastroesophagic reflux disease and Helicobacter pylori eradication may be optimized by the analysis of polymorphisms of the CYP2C19 gene. Additionally, the study of variants of IL28 helps in the identification of patients with more chances of response to the treatment of hepatitis C with interferon and ribavirin. The analysis of polymorphisms of the gene coding for the enzyme thiopurine methyl transferase (TPMT) helps in the reduction of the risks associated with the use of azathioprine in the treatment of inflammatory bowel disease. In this way, pharmacogenomics constitute not only a therapeutic tool that already shows an impact in the individualization of drug use in gastroenterology but also a tool with a great projection in the future.