This chapter discusses the integrations of the nanoparticles with microfluidic platforms for biological diagnosis. It evaluates the applications of two emerging formats of microfluidics, digital microfluidics and paper‐based microfluidics, for biological diagnosis. Microfluidics is an enabling technology that can be employed in numerous biological studies because of its high‐throughput, precision, sample efficiency, portability, and low‐cost production. Many investigations are currently underway concerning the imaging of the biological molecules and cellular components using fluorescent nanomaterials. The main problems associated with fluorescence methods can be addressed by using semiconductor quantum dots (Qdots) possessing unique optical properties. Their surface is capable of being modified with various biomolecules making them selective to different analytes. In the bioanalysis with Qdots, these nanoparticles are conjugated with biomolecules for the detection of analytes. In the case of a disease, the target analytes can be viruses, antigens, and cancer biomarkers, whose concentration is also of interest.