An approach to performing in-line extraction employing functionalized magnetic particles for CE and microchip electrophoresis is presented. Silica-coated iron oxide particles were synthesized and used as the solid support. The particles were functionalized with octadecylsilane and used as reverse-phase sorbents for in-line SPE followed by electrophoresis. Magnets were used to locally immobilize these sorbents inside the capillary or microchip. Extraction, elution, and detection of the analytes were performed sequentially without interruption or need for sample handling. Mixtures of hydrophobic analytes were successfully extracted from solution using the synthesized magnetic sorbents. CE was able to extract and separate mixture of parabens within 10 min. In-line extraction was also carried out on a disposable PMMA microfluidic device with LIF detection. Electrophoretic separation of fluorescent dyes, Rhodamine 110 and SulfoRhodamine B, was completed in under a minute. The results demonstrated the feasibility of performing the in-line extraction/separation technique in a microchip platform enabling rapid analysis, low sorbent consumption, and increased analyte recovery (relative to the capillary format).