The application of nanoparticles for the delivery and targeting of pharmaceutical, therapeutic and diagnostic agents in cancer therapy has received significant attention in recent years. Nanoparticles may be constructed from a wide range of materials and used to encapsulate or solubilize chemotherapeutic agents for improved delivery in vivo or to provide unique optical, magnetic and electrical properties for imaging and therapy. Several functional nanoparticles have already been demonstrated, including some clinically approved liposome drug formulations and metallic imaging agents. The next generation of nanoparticle-based research is directed at the consolidation of functions into strategically engineered multifunctional systems, which may ultimately facilitate the realization of individual therapy. These multiplexed nanoparticles may be capable of identifying malignant cells by means of molecular detection, visualizing their location in the body by providing enhanced contrast in medical imaging techniques, killing diseased cells with minimal side effects through selective drug targeting, and monitoring treatment in real time. This article highlights recent progress in the design and engineering of multifunctional systems, as well as discusses the development of a new, scalable and economic method for the modular preparation of multiplex nanoparticles where functional properties can be precisely and simply tailored.