Abstract: A device for combined bioaffinity assay and electrophoretic separation is provided, which comprises a capillary system having two stages, a first stage in which bioaffinity interactions of analyte molecules and molecular recognition elements are performed, and a second stage, in which electrophoretic separation of the analyte molecules and subsequent detection of the separated species is accomplished. Within the first capillary stage the molecular recognition elements are attached and immobilized to the inside capillary wall, for example, by adsorption or by covalent binding to the capillary material. The method for combined bioaffinity assay and electrophoretic separation comprises flowing an analyte through a capillary system having two stages. In a first capillary stage the analyte molecules are captured by respective molecular recognition elements present in that stage.