The nanomaterial industry is currently expanding, driven by the diversity and versatility of applications in which they can be found. Nanomaterials (NMs) can have a variety of uses ranging from solar cells and pigments to sunscreen, body implants and nanomedicines among others. Much concern has arisen regarding their safety to humans however, as experimental studies show that exposure with NMs may lead to health effects such as chronic inflammation, cardiovascular diseases, fibrosis and even cancer. Health effects on workers is one of the major concerns since workers potentially may face high exposures at occupational settings. However, most of the studies available are performed with acute exposures and high doses which do not reflect real work environment exposure situations. Currently, the molecular mechanisms of toxicity of these NMs are still unknown. The purpose of this study was to investigate the mechanisms of toxicity of two carbon nanotubes (NM400 and NM401) and one titanium dioxide (NM104) possessing different physicochemical properties. The study focused on pulmonary effects and cellular responses by way of an in vitro model of human lung epithelial cells (HBEC-3KT). It attempts to address occupational settings employing low doses and short-term acute and long-term chronic exposures. Characterization of the analyzed NMs was done by dynamic light scattering. The molecular signature of the NMs was investigated by use of a custom and focused gene expression array designed to analyze target genes from signaling pathways related to lung inflammation, fibrosis and cancer. Furthermore, Comet Assay was used to study oxidative DNA damage. The results indicated altered gene expression for various genes depending on exposure time, type of NM, and dose used. NM401-exposed cells showed the highest number of regulated genes while NM104-exposed cells showed the lowest. Similar and differential molecular signatures were found between the three NMs. While NM400 and NM401 are both carbon nanotubes, they showed different effects. NM400 had more similar effects as NM104 which is a titanium dioxide. However, more work is needed to elucidate the various molecular mechanisms involved.