Microfluidic is an ensemble of technologies and methods that permits the handling and analysis of minute volumes of samples in short timescales. Since its introduction it revealed a remarkable potential to unveil novel biological mechanisms. The small volumes involved in microchannels shortens reaction time and foster interactions between bioanalytes. Furthermore, the reduced footprint of the microfluidic channels also allows the integration of different modules within the same chip, each performing a dedicated step of a complex procedure, in what was defined as a lab-on-a-chip (LOC) platform. The use of 3D dimensional particles in such devices serve a double purpose: the manipulation of biological sample such as single cells in suspension and the introduction of microbeads that exhibits high surface-to-volume ratios and hence improved analyte collection. In this thesis, we present the development of new tools for the accurate manipulation of microparticles in microfluidic channels and their efficient exposure to flow. Microbeads or single cells were immobilized on-chip via a combination of hydrodynamic and dielectrophoretic (DEP) effects. Following their trapping, single-cells could be selectively released and recovered off-chip for further expansion and characterization. A transcriptomic analysis of recovered cells revealed marginal alteration of their molecular profile upon exposure to DEP forces and thus validated the potential of our technology for the assessment of single-lymphocytes properties. The efficient analyte collection achieved by microfluidic systems could benefit the field of diagnostics through the introduction of two distinct platforms. The first employs DEP forces to carry out the simultaneous detection of two acute kidney injury markers, NGAL and Cystatin C, in a minimally diluted buffer. High aspect-ratio three-dimensional electrodes were integrated in a microfluidic channel and could generate sufficient forces to retain functionalized beads against the flow of reagents for a 15 minutes-long incubation. The second introduces a novel approach based on DNA barcodes and toe-hold mediated strand displacement to perform the rapid readout of highly multiplexed immunoassays. The signal acquisition takes place in a wide microchamber crowded with mechanical traps stopping the beads at dedicated locations, its duration could be shorten down to 3 minutes per marker, with a throughput approaching 20 markers per hour. The obtained results demonstrated the potency of microfluidic platform for the manipulation and analysis of microparticles in-flow and paves the way for the development of a novel generation of highly integrated lab-on-a-chip systems.