Amongst the engineered nanomaterials, especially carbon nanotubes (CNTs) have received considerable attention for application in tissue engineering scaffolds. CNTs are considered promising on behalf of their physicochemical properties, yet such nanomaterials also have been associated with potentially hazardous effects on human health. To gain insight into the toxicity aspects of CNTs in vivo, the present study presents a systematic review of literature. After screening of literature through defined inclusion and exclusion criteria, and subsequent data extraction, it can be concluded that pulmonary administered CNTs have the capacity to induce toxicity in the lung area. However, conclusions for other organs, or on systemic toxicity, are yet premature. In addition, the carcinogenic potential of CNTs is also still ambiguous, because contradictive results are presented. Intrinsic factors, such as material characteristics, and associated distribution and agglomeration patterns influence the toxic potential of CNTs. Similarly, environmental factors such as the exposure route, preexisting allergies, pathological infections, or air pollutant exposure are significant. Despite the many reports published currently, more studies will be required to gain full understanding of the toxic potential of CNTs and especially the underlying mechanisms. For this end, development of standardized protocols and reliable nanodetection techniques will form prerequisites.