There is great interest for developing poly(lactide-co-glycolide) (PLGA) based particles for targeted delivery and controlled release of encapsulated biological molecules. These PLGA particles can be used to deliver proteins, small molecule drugs and nucleotides. Furthermore, it has been shown that the co-encapsulation of multiple factors in PLGA particles can generate synergistic responses, and can also provide theranostic capability. However, the number of possible unique particle formulations that may be generated by the combination of different components in a particle increases dramatically with each new component, and currently, there is no method to generate large libraries of unique PLGA particles. In order to address this gap, we have developed a high-throughput methodology to produce hundreds of small batches of particles. The particles are generated in multi-well plate wells by a modified oil-in-water emulsion technique. In order to demonstrate the versatility of this technique, combinatorial formulations of six different loading concentrations of three fluorescent dyes were fabricated giving rise to 216 unique PLGA particle formulations. We demonstrate systematic and well-controlled combinatorial loading of hydrophobic molecules into the particles. This parallel particle production (PPP) methodology potentiates the generation of hundreds of different combinatorial particle formulations with multiple co-encapsulates in less than 24 h in standard polystyrene multi-well plates, thus providing rapid, low cost, high-throughput production. We envision that such a PPP library of particles encapsulating combinations of drugs and imaging modalities can subsequently be tested on small populations of cells in a high-throughput fashion, and represents a step toward personalized medicine.