A new methodology is proposed to automate the monitoring of sulfonamide residues in milk samples. It combines a screening unit for the total amount of sulfonamide with capillary electrophoresis-mass spectrometry (CE-MS) equipment for processing the samples containing a detectable level of sulfonamide. The screening unit consists of continuous-flow system (CFS) to precipitate the proteins connected on-line to the CE-MS equipment, in which a common characteristic ion of all sulfonamides was monitored with the MS detector by flushing the sample through the capillary. The confirmatory method is based on the purification and preconcentration of sulfonamides in a CFS unit and posterior analysis by CE-MS. The sample treatment unit was also on-line connected to the CE-MS equipment. In order to increase sensitivity, the flow rate of the sheath liquid was diminished from 0.5 to 0.2 microL.min(-1) by increasing the content in water from 0 to 50% and the formic acid from 0.5 to 1.5% in this liquid and by applying an overimposed pressure of 5 mbar during the electrophoretic separation. The method allowed the analysis of 30 samples per hour.