Presented is a novel approach for an integrated micro total analysis system (μTAS) based on a microfluidic on-chip device that supports ultrasensitive confocal detection of fluorescent cells and particles and subsequently allows for their precise sorting in the fluid phase with respect to spectroscopic properties, such as brightness and color. The hybrid silicone elastomer/glass chip first comprises a branched channel system to initiate fluid mixing and to hydrodynamically focus the sample solution down to a thin flow layer, matching the size of the confocal detection volume placed at that position and, thus, providing a high detection efficiency. In the subsequent on-chip module, the dispersed cells or particles can be sorted into two different output channels. The sorting process is realized by a perpendicular deflection stream that can be switched electrokinetically. The performance of the automated sorting routine is demonstrated by precise partition of a mixture of differently colored fluorescent beads. Moreover, the specifically branched channel geometry allows for direct implementation of reaction steps prior to detection and sorting, which is demonstrated by inducing a selective recognition reaction between the fluorescent protein R-phycoerythrin and a mixture of live bacterial cells exhibiting or lacking the respective surface antigens.