Capillary electrophoresis (CE) of chitooligosaccharides (COS) in aqueous solution is effective for their separation from other saccharides. However, COS easily adsorb on negatively charged surfaces, such as fused silica capillaries in acidic solutions. Conventional photometric detection cannot be applied directly because saccharides do not absorb ultraviolet or visible light. Here, we describe a simple CE of COS in an acidic solution using a positively charged capillary coated with N-trimethoxypropyl-N,N,N-trimethylammonium chloride and indirect photometric detection with crystal violet nitrate background solution.