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The use of glass and PDMS microchips has been investigated to perform rapid and efficient separation of allergenic whey proteins by IEF. To decrease EOF and to limit protein adsorption, two coating procedures have been compared. The first one consists in immobilizing hydroxypropyl cellulose (HPC) and the second one poly(dimethylacrylamide-co-allyl glycidyl ether) (PDMA-AGE). EOF limitation has been evaluated using frontal electrophoresis of a fluorescent marker of known effective mobility. EOF velocity was decreased by a factor about 100 and 30, respectively. pH gradient formation has been evaluated for each microchip using fluorescent pI markers. It was demonstrated that as expected a coating was essential to avoid pH gradient drift. Both coatings were efficient on glass microchips, but only PDMA-AGE allowed satisfying focusing of pI markers on PDMS microchips. Fluorescent covalent and noncovalent labelings of milk proteins have been compared by IEF on slab-gels. IEF separation of three major allergenic whey proteins [beta-lactoglobulin A (pI 5.25) and B (pI 5.35) and alpha-lactalbumin (pI 4.2-4.5)] was performed in both microchips. Milk proteins were separated with better resolution and shorter analysis time than by classical CIEF. Finally, better resolutions for milk allergens separation were obtained on glass microchips.