Short-chain fatty acids (SCFA) are compounds produced during fermentation of gut microbiota. Acetic, propionic and butyric acids are the most important SCFA produced from non-digestible foods. We developed and validated a rapid and low-cost capillary electrophoretic (CE) method for determination of acetic, propionic and butyric acids in mice feces (100 mg of sample). Electrophoretic separation was performed for SCFA determination in feces samples during 10 min. The method showed good linearity for all analytes (determination coefficient, r2 > 0.98); recovery from 74.1 to 109.8%, while the intra- and interday precision essays were suitable (relative standard deviation (RSD) < 10%); and limits of detection and quantification of 0.13-0.43 mM for acetic acid, 0.09-0.29 mM for propionic acid and 0.03-0.09 mM for butyric acid. Real samples of mice dextran sulfate sodium-induced colitis feces treated with jabuticaba (Plinia cauliflora) aqueous extract were performed successfully.