A fast, simple and quantitative approach was established for monitoring autophagy in HeLa cells by directly detecting the conversion of green fluorescent protein (GFP) labelled autophagy markers, GFP-LC3-I to GFP-LC3-II, in crude cellular extract using capillary electrophoresis (CE) with laser-induced fluorescence (LIF). Compared with the traditional methods, this proposed method is simpler and more reliable. Moreover, high sensitivity, with a limit of detection (LOD) of 0.48 ppt (bovine serum albumin as standard protein), was obtained by an in-capillary derivatization method coupled with a field-enhanced sample injection (FESI) technique, this may allow the success of this technique in the detection of endogenous markers of autophagy in cells.