The influence of organic modifier on the separation of six biogenic amines in capillary zone electrophoresis was investigated using ammonium acetate as a background electrolyte. The electrophoretic mobility of each biogenic amine at a given pH decreases to a different extent on addition of organic modifier which may lead to alteration of the migration order. The results indicate that addition of acetonitrile (30%, v/v) or methanol (40%, v/v) to ammonium acetate buffer (100 m M) at pH 7.5 effects the resolution of co-migrating biogenic amines. Complete separation of six biogenic amines was achieved in short times using a 44 cm×50 μm I.D. fused-silica capillary at 10 kV. Methanol is relatively less effective than acetonitrile as an organic modifier to separate these biogenic amines.