The explosive growth of nanotechnology in the last years has led to dramatic innovations in pharmacology, and it is revolutioning the development of biologically active compounds. Carbon nanotubes (CNTs) are widely explored for biomedical applications such as intracellular transporters for (bio)molecules, and represent promising future tools for efficient and safe cell therapy. Due to their nanoscale dimensions, the ability to interact with cells, and their easy functionalization, CNTs are close-to-ideal vectors for an efficient and safe cell therapy, obviating the risks associated with the use of viral vectors. Notwithstanding, conflicting data concerning the biocompatibility of CNTs have been reported in the literature; while some studies point toward very low toxicity of CNTs both in vitro and in vivo, others reveal various toxic effects such as oxidative stress, DNA damage, and cell apoptosis. Thus, standardized methods and independent test systems are urgently needed to verify cytotoxicity data in this research field. In this chapter, we summarize the used methods and the achieved main results in our laboratories concerning multiwalled carbon nanotubes (MWCNTs) biocompatibility studies. The in vitro response of human neuroblastoma cell line and primary mouse neurons was investigated following the exposure to different samples of MWCNTs in order to evaluate their effects on cell viability, oxidative stress, and apoptosis. Moreover, in vivo neurocompatibility tests were carried out through injections in mouse brains.