Capillary electrophoresis (CE) coupled with capacitively-coupled contactless conductivity detector (C4D) is considered as an analytical method with some advantages as simple equipment, saving of time and consumable chemicals. This method can be useful for the simultaneous analysis of multi-ions in liquid matrix. This study describes the using of CE-C4D system for determination of short chain fatty acids in biodiesel as the corresponding anions in order to monitor the concentration increase of these acids during the storage process of biodiesel. Samples were treated by liquid-liquid extraction, and then the aqueous phases were removed and analysed by CE-C4D system. The background electrolyte (BGE) was composed of 10mM L-histidine (His)/2-(Nmorpholino)ethanesulfonic (MES) acid, pH 5.6, and 0.02mM cetyltrimethylammonium bromide (CTAB). In the experiment conducted in 20 days, biodiesel was added with no antioxidants and stored under normal conditions. The results showed that the concentrations of formic acid, acetic acid, and propionic acid in biodiesel varied from 6.86-33.2 mg/kg, 7.99-16.0 mg/ kg, and 1.53-5.77 mg/kg, respectively, leading to the elevation of acid index from 0.0169 to 0.0597 mg KOH/g.