A new method involving zinc sulphate deproteinization was developed to study short chain fatty acids (SCFA) production in the colon and subsequent occurrence of SCFA in blood. SCFA were baseline separated in a 30min cycle using ion-exclusion chromatography and detected by mass spectrometry. Concentrations could be measured down to 10muM and isotopomeric distributions could be assessed, enabling the conduction of tracer studies to study changes in SCFA synthesis. The applicability of the method was tested in an extensively characterized pig model yielding portal SCFA concentrations ranging from 70muM (butyric acid) to 150muM (propionic acid) to 440muM (acetic acid) prior to butyrate tracer infusion, reaching butyric acid isotopic steady state within 2h. AD - Department of Surgery, Maastricht University, Nutrition and Toxicology Research Institute Maastricht, P.O. Box 616, 6200 MD Maastricht, The Netherlands; Wageningen Centre for Food Sciences, P.O. Box 557, 6700 AN Wageningen, The Netherlands.