The use of nanoparticles (NPs) in immunodiagnostics is a challenging task for many reasons, including the need for miniaturization. In view of the development of an assay dedicated to an original, miniaturized and fully automated immunodiagnostics which aims to mimic in vivo interactions, magnetic zwitterionic bifunctional amino/poly-ethyleneoxide maghemite core/silica shell NPs functionalized with allergenic a-lactalbumin were characterized by CE. Proper analytical performances were obtained through semi-permanent capillary coating with didodecyldimethylammonium bromide (DDAB) or permanent capillary wall modification by hydroxypropylcellulose. The influence of experimental conditions (e.g. buffer component nature, pH, ionic strength, and electric field strength) on sample stability, electrophoretic mobility, and dispersion was investigated using either DDAB- or hydroxypropylcellulose-coated capillaries. Adsorption to the capillary wall and aggregation phenomena were evaluated according to the CE conditions. The proper choice of experimental conditions, i.e. separation under -10 kV in a 25 mM ionic strength MES/NaOH (pH 6.0) with a DDAB-coated capillary, allowed the separation of the grafted and the non-grafted NPs.