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Microfluidics plays a key role in the design of automated platforms for realizing biological assays in a miniaturized format. Several advantages are offered by a microfluidic system, namely, low sample and reagent consumption (typically a few microliters), the possibility to mass-produce and to integrate several analysis modules enabling portable automated applications, fast analysis and low cost. Furthermore, the combination of advanced Complementary Metal-Oxide-Semiconductor (CMOS) technology and microfluidics can result in flexible and easy-to-use hybrid systems that hold large potential for application in an analytical laboratory or at the point-of-care. In this Thesis, two different monolithic silicon CMOS chips were designed, fabricated and tested, demonstrating state-of-the-art performance utilising a novel fluorescence detection principle. They allowed the detection of monoclonal antibodies in a solution or the precise counting of specifically labelled fluorescent cells in a mixed-cell sample. The proposed detection method does not require the utilization of a fluorescence camera and filter set. The first part of this Thesis presents different methods, fabrication processes and materials for microfluidic cartridges that can be integrated in a hybrid way with silicon CMOS chips. Glass and SU-8 capillaries are tested, a novel material (NOA 63) is proposed for fabricating a natively hydrophilic microfluidic cartridge, and the fabrication of custom-designed polydimethyl(-siloxane) (PDMS) cartridges for easy integration on top of a CMOS chip is introduced. The second part of this Thesis presents the combination of microfluidics with a monolithic and fully-integrated CMOS chip for the manipulation and detection of fluorescent magnetic beads, inside a PDMS microchannel that is loosely positioned on top of the chip. Magnetic manipulation is done by current actuation of microcoils on the chip; detection is achieved using single photon avalanche diodes (SPADs), located in the centre of each microcoil, that count the fluorescent photons originating from a single labeled magnetic bead. This approach permits in principle microscope-less fluorescence detection with high sensitivity. Using sandwich immunoassays on the beads' surfaces, the selective detection of the cancer biomarker 5D10 monoclonal antibody (mAb) from a non-purified hybridoma cell-culture medium is demonstrated. In the third part, a CMOS chip comprising a matrix of SPADs is designed, fabricated and tested. The recognition of single fluorescently-labelled cells from the breast cancer cell line MCF-7 in a test solution of mixed MCF-7 and non-fluorescent Jurkat cells is demonstrated, without the need of a bulky and expensive fluorescent microscope setup. Moreover, due to the use of a SPAD matrix spanning the complete width of the microchannel, the system does not require any cell focusing mechanism, needed when using a single detector. This allowed the use of a very simple, easily replicable and disposable plastic microfluidic cartridge.