Due to their unique mechanical, electronic and chemical properties, carbon nanotubes (CNTs) have been promising candidates for a wide variety of revolutionary applications in information, photovoltaic, energy, sensors, materials, medicine and so on. Meanwhile, with the increasing large-scale production and application of CNTs, their bio-safety assessment has raised wide attention. Although there is considerable experimental data of CNT pulmonary toxicity at the molecular, cellular and whole animal levels, many conclusions are inconsistent and in some cases directly conflicting. The conflicting reports can be attributed to real sample-to-sample variation in material properties, such as types and contents of metal impurities, dispersity, aspect ratio, etc.. In this review, we describe recent research progress on respiratory toxicity of CNTs and its cellular mechanisms, which may depend on the structure and properties of CNTs. Furthermore, many factors that may affect cytotoxicity of CNTs are summarized and discussed here. Finally, we provide a prospect to the future work on studying and evaluating pulmonary toxicity of the CNTs systematically and scientifically.