Avidin-biotin interaction is one of the strongest non-covalent interactions in the nature. Avidin and its analogues have therefore been extensively utilized as probes and affinity matrices for a wide variety of applications in biochemical assays, diagnosis, affinity purification, and drug delivery. Recently, there has been a growing interest in exploring this non-covalent interaction in nanoscale drug delivery systems for pharmaceutical agents, including small molecules, proteins, vaccines, monoclonal antibodies, and nucleic acids. Particularly, the ease of fabrication without losing the chemical and biological properties of the coupled moieties makes the avidin-biotin system a versatile platform for nanotechnology. In addition, avidin-based nanoparticles have been investigated as diagnosis systems for various tumors and surface antigens. In this review, we will highlight the various fabrication principles and biomedical applications of avidin-based nanoparticles in drug delivery and diagnosis. The structures and biochemical properties of avidin, biotin and their respective analogues will also be discussed.