A constant theme weaving through the history of science, technology, and medicine is that the law consistently lags behind innovation. By the time we understand the science and technology involved, there is already another more advanced and complex product in the pipeline or entering the market. One area where this is proving particularly acute is nanotechnology. Nanotechnology and nanoscience have facilitated breakthroughs in the pharmaceutical and medical device realms, enabling cutting-edge treatments. Not surprisingly, innovations at the intersection of nanotechnology and medicine have inundated the United States Patent and Trademark Office (USPTO) with patent applications. The USPTO has implemented a nanotechnology classification system for review and categorization purposes. However, problems of overlapping claims and complicated scientific aspects will largely be left to courts to sort out a clumsy forum for determination of complex patent law issues that arise based on scale, size, and interactions at the nanoscale that transcend previously envisioned physical and chemical boundaries. As nanopatenting continues, the USPTO and courts will increasingly face three core problems: (1) limitations of and inconsistencies among current definitions of nanotechnology; (2) uncertainty and lack of uniformity in measurement capabilities regarding critical aspects of size, properties, and characteristics at the nanoscale; and (3) the role of patent claims to accurately and consistently encapsulate and distinguish the scope of nanotechnology inventions. Given the Supreme Court’s recent interest in questions of patentability and appropriate claim scope of genetic inventions, the time is ripe for the USPTO to extract lessons for nanotechnology. This article will utilize the recent district court case Elan Pharma v. Abraxis Bioscience involving the blockbuster nanotechnology cancer treatment Abraxane to illustrate inherent problems with the USPTO nanotechnology classification system and will suggest a research agenda of steps that might be taken to assist the USPTO in fulfilling its mission to foster and reward innovation while also assisting in broader efforts to gather nanotechnology information.