Capillary electrophoresis (CE) was interfaced with a quadrupole mass spectrometer, using pneumatically-assisted electrospray ionization (ESI) in order to analyze Ecstasy and derivatives in urine. The influence of the sheath liquid composition, including the type and the percentage of the organic solvent, as well as the nature of the conductive acid modifier, were examined in order to find optimal coupling conditions. A fractional factorial design was also used to optimize the electrospray experimental parameters, such as the nebulizing gas pressure, the electrospray voltage, the drying gas flow rate, the drying gas temperature, the skimmer voltage, and the sheath liquid flow rate. The separation conditions were optimized in terms of temperature, electrolyte concentration, percentage of organic modifier, as well as capillary type. Finally, the optimal CE-ESI-MS conditions were applied to the analysis of Ecstasy and other related amphetamines in urine samples, following a liquid-liquid extraction procedure.