Nano-engineered materials such as carbon nanotubes (CNTs) have gained attention due to their many characteristics which make them the ideal material for applications in biomedical areas. The potential use of CNTs in medical applications is promising but their interaction with the human body and the effects of those interactions are still uncertain. The results of such interactions often determines the clinical success of nano-engineered materials such as CNTs in the medical field; therefore, the aim of this study was to measure the biocompatibility of two types of CNTs with human umbilical artery endothelial cells (HUAEC) and human hepatoma cells (HepG2). The genotoxic and mutagenic activity of pristine and N-doped CNTs was evaluated by trypan blue exclusion test, flow cytometry, chromosomal aberrations, cell cycle dynamics by mitotic inhibition and by flow cytometry as well as single cell gel electrophoresis (SCGE). Data was analyzed by both one-way and two-way analysis of variance (ANOVA) when appropriate, Student's t, Kruskall–Wallis and the chi-squared test (X2) based on data characteristics. Ruptures in the cell's DNA were evidenced by the SCGE on HUAEC and HepG2 cells when exposed to sub-lethal concentrations of both types of CNTs. Results obtained for the cell viability, the cell cycle dynamics and the chromosomal aberrations were not significantly different when compared to the negative control. These findings suggest an increased risk of fixed mutations since the cells continue through the cell cycle although their DNA is compromised.