A study on the simultaneous separation of 13 pharmaceutical products by capillary electrophoresis with capacitively coupled contactless conductivity detection was presented. The parameters of the background electrolyte, such as pH, organic additives as well as types and concentrations of cyclodextrins (CD) were studied. The optimal separation conditions were achieved with a background electrolyte consisting of 9 mM Tris/5 mM lactic acid at pH 8.0, containing 5% n-propanol, 0.025% gamma-CD, 0.075% hydroxyl-beta-CD and 0.15% dimethyl-beta-CD. Limits of detections ranged from 61 to 1676 mu g/L (S/N = 3) and the relative standard deviations for migration time and peak area were below 2 and 6%, respectively. This demonstrated the potential of the capillary electrophoresis-capacitively coupled contactless conductivity detection method for biomedical and environmental analysis, as shown in the determination of pharmaceuticals identified as emerging pollutants in water samples.