Microdialysis is used for in vivo sampling of extracellular molecules. The technique provides a continuous and dynamic view of concentrations of both endogenous released and exogenous administered substances. Microdialysis carries a low risk of complications and has proven to be a safe procedure in humans. The technique has been applied in several clinical areas, including gastrointestinal surgery. Microdialysis may be used for studies of tissue metabolism, and the technique is also a promising tool for pharmacological studies of drug penetration into abdominal organ tissue and the peritoneal cavity. The clinical significance of intraabdominal microdialysis in postoperative monitoring of surgical patients has yet to be proven. In this review, we introduce the microdialysis technique, and we present an overview of theoretical and practical considerations that should be taken into account when using microdialysis in intraabdominal clinical research.