Background: The present study evaluates whether microdialysis of glycerol and lactate reflects mucosal injury and permeability changes after strangulation obstruction of the pig small intestine. Methods: Strangulation obstruction was induced by tightening a rubber band around a small bowel loop until its venous pressure increased to a level just below diastolic aortic pressure (partial strangulation), or further until cessation of flow in the main feeding artery (total strangulation). Mucosal injury and permeability of marker molecules from blood to lumen and vice versa was compared to release of glycerol and lactate to the intestinal lumen. Results: Mucosal injury, hyperpermeability, and release of glycerol were more pronounced after total than after partial strangulation. In animals with partial strangulation there was a complete restitution of the surface epithelium, and luminal glycerol and lumen-to-blood permeability of polyethylene glycol 4000 remained low. Such animals showed a sustained elevation of lactate and blood-to-lumen permeability of fluorescein isothiocyanate dextran after 2 h of partial strangulation, but a decline to baseline levels of these parameters in animals with 1 h partial strangulation. Conclusion: Microdialysis of lactate and glycerol in the intestinal lumen may be used to assess structural and functional changes of the intestinal mucosa after strangulation obstruction.