In anaerobic digestion of organic matter, several metabolic pathways are involved during the simultaneous production and consumption of short-chain fatty acids (SCFA) in general and acetate in particular. Understanding the role of each pathway requires both the determination of the concentration and isotope enrichment of intermediates in conjunction with isotope labeled substrates. The objective of this study was to establish a rapid and simple GC/MS method for determining the isotope enrichment of acetate and concentration of underivatized short-chain fatty acids (SCFA) in biogas digester samples by direct liquid injection of acidified aqueous samples. Sample preparation involves only acidification, centrifugation and filtration of the aqueous solution followed by direct injection of the aqueous supernatant solution onto a polar column. With the sample preparation and GC/MS conditions employed, well-resolved and sharp peaks of underivatized SCFA were obtained in a reasonably short time. Good recovery (96.6-102.3%) as well as low detection (4-7 µmol/L) and quantification limits (14-22 µmol/L) were obtained for all the 6 SCFA studied. Good linearity was achieved for both concentration and isotope enrichment measurement with regression coefficients higher than 0.9978 and 0.9996, respectively. The method has a good intra- and inter-day precision with a relative standard deviation (RSD) below 6% for determining the tracer-to-tracee ratio (TTR) of both [2-(13)C]acetate and [U-(13)C]acetate. It has also a good intra- and inter-day precision with a RSD below 6% and 5% for determining the concentration of standard solution and biogas digester samples, respectively. Acidification of biogas digester samples with oxalic acid provided the low pH required for the protonation of SCFA and thus, allows the extraction of SCFA from the complex sample matrix. Moreover, oxalic acid was the source of formic acid which was produced in the injector set at high temperature. The produced formic acid prevented the adsorption of SCFA in the column, thereby eliminating peak tailing and ghost peaks. The applicability of the validated GC/MS method for determining the concentration of acetate and its (13)C isotope enrichment in anaerobic digester samples was tested and the results demonstrated the suitability of this method for identifying the metabolic pathways involved in degradation and production of acetate.