Demand for carbon nanotubes (CNTs) is increasing rapidly in electrical, mechanical, and health and medical applications due to their thermal, electrical conductive and other properties. The continued commercial up-scaling of CNT production and application needs to be accompanied by an understanding of the occupational health, public safety and environmental implications of these materials. An increasing volume of literature on the toxicity of CNTs is being published; however, the results of these studies are frequently inconclusive. Due to the enormous number of permutations of nanoparticle shape, dimensions, composition and surface chemistry, only a fundamental understanding of the processes by which CNTs interact with cells will allow a realistic, practical assessment of the risks of the wide range of possible products. Alternatively, by understanding how the physicochemical properties of CNTs relate to their interaction with cells, it will be possible to design 'medical grade' CNTs, which can be used as diagnostic agents or as vectors to deliver therapeutic agents to cell and tissue targets. This article discusses the challenges associated with characterizing the toxicity of CNTs and the need for complimentary nanometrology techniques to relate their physicochemical properties to their toxicity.