The factors influencing the separation of metallothioneins (MTs) by capillary zone electrophoresis (CZE) were studied using untreated fused-silica capillaries. A comparison was made between the various buffers of 20 mM Na2B4O7, 10 mM Na2B4O7-10 mM Na2HPO4 and 20 mM Na2B4O7-10 mM Tris for the separation of MTs in terms of migration time and UV-absorbance under the various applied voltages. The migration times for MT-I and MT-II decreased with increase in the applied voltage and column temperature. However, no significant change in UV absorbance was observed. When Na2B4O7-Tris buffer was chosen for the separation of MTs, the migration time, UV absorbance, theoretical plates and resolutions also increased with increasing buffer concentrations. The effect of buffer pH on migration time was relatively complicated. Under the optimal operating conditions the standard MTs were well separated. Determination of MTs in the real samples failed due to the adsorption of other proteins onto the capillary walls.