An original micropillar array dedicated to electrophoretic separations has been developed. It consists of a rectangular zone of PDMS micropillars protruding on a PDMS block. This area has been chosen to mimic a diluted gel structure and remains uncovered to keep the ability to perform an immunoblot after the protein separation for further applications in the field of allergy diagnosis. The micropillar array geometry has been optimized by evaluating the influence of pillar shape, pillar size and interpillar distance on evaporation and IEF separation. The separation conditions namely electrolyte composition, temperature and sample loading have been studied. Finally a protein mixture with pI ranging from 4.7 to 10.6 has been successfully separated within this microdevice by IEF without decreasing the resolving power obtained with conventional minigel. The micropillar array developed for electrophoretic separations leads to much shorter analysis times and can be reused several times while gels are disposable.