Many recently designed drug delivery systems have been constructed from nano-sized components that serve as the carrier or targeting ligand for a therapeutic agent. Even though these materials have been regarded previously as inert or non-active components of dosage forms, they are now recognized as sometimes being even more important than the drug itself. Hence, it is becoming increasingly imperative that the pharmaceutically relevant properties, including identity, physicochemical characteristics, purity, solubility and toxicity, of these functional nano-excipients be fully characterized. Carbon nanotubes (CNTs) are novel nanomaterials made of carbon atoms that have wide application potential in many areas of nanomedicine. However, because of their significant potential, CNTs, as building blocks for nanomedicines, need to be characterized more fully. Studies to date indicate that both physical and chemical properties of CNTs play an important role in their interactions with cells. Therefore, a full understanding of the physical properties of CNTs, such as identity, chirality, particle size, aspect ratio, morphology and dispersion state, as well as chemical properties such as purity, defect sites and types and functional groups, will be essential to develop a full characterization panel of these versatile nanomaterials.