Essential in biomedical research is the necessity of gathering statistically relevant data about large populations of specific biological entities,€ e.g. organisms, cells or molecules, while preserving detailed information about each single entity under investigation. This thesis deals with this need and proposes the combination of microfluidics and micro-arraying€ techniques in developing technological tools to conceive bio-assays at single molecule/cell/organism resolution. First, we propose an on-chip immunoassay technique, through which we demonstrated detection of the biomarker tumor necrosis factor alpha in serum down to concentrations in the attomolar range (10-18 M). In particular, we provide a comprehensive predictive model of the assay, which employs micro-arrays of superparamagnetic beads. We introduce the concept of €œmagnetic particle-scanning€, as a method for building immunoassays with extremely low limit of detection, down to the single-molecule level. Afterwards, we modified our bead micro-arraying technique, to make it suitable for the immobilization of particles and cells of various sizes and properties. Specifically, we present a method for the electrostatic self-assembly of dielectric microspheres in well templates, as a technique for fast and versatile fabrication of microlens arrays. By combining these arrays with microfluidics, we created a new tool for single-nanoparticle detection in flowing media, able to detect moving objects of sub-diffraction size through conventional low-magnification microscopes. An analogous micro-arraying method was then developed to seed large populations of non-adherent cells in isolated micro-compartments. In combination with an electrowetting-on-dielectric microfluidic platform, this technique allows implementing high-throughput cytotoxicity assays on yeast cells, at single-cell resolution. Subsequently, we conceived technological solutions for the automated analysis of Caenorhabditis elegans, one of the most employed model organisms in biomedical research. First, we developed a microfluidic platform for on-chip nematode culture and creation of synchronized C. elegans embryo micro-arrays. Long-term multi-dimensional imaging in our device allows systematic phenotyping studies at single-embryo resolution. We could discriminate embryonic development variations with unprecedented accuracy and we successfully analyzed the impact of perturbations of the mitochondrial functions on the embryogenesis. A €œsecond generation prototype€ of the device is then presented, enabling long-term automated studies on C. elegans at single-nematode resolution and over the whole organism development, from early embryogenesis to adulthood. Finally, we introduce a €œthird generation prototype€, which features: (i) a new microfluidic design tailored for the isolation of larvae at a desired developmental stage and for their successive culture and treatment; (ii) a method for reversible immobilization of nematodes, enabling long-term high-resolution imaging. We successfully employed this platform to analyze protein aggregation in a C. elegans model for human amyotrophic lateral sclerosis (ALS). The device allows precisely localizing protein aggregates within the nematode€™ tissues, as well as monitoring the evolution of single aggregates over consecutive days at sub-cellular level.