Nanoparticles are being explored for biomedical applications in diagnostics and therapeutics. However, biocompatibility, toxicity and cellular entry ability are critical factors that will determine the utility of nanoparticles in clinical applications. “Omics” technologies can provide powerful tools that are sensitive and complementary for the study of molecular toxicology and for biomedical applications of nanomaterials. Specifically, proteomics could elucidate mechanisms of action and contribute to studies on how nanomaterials affect protein expression in tissues and organs, metabolic pathways, signal transduction mechanisms and target molecules. The objective of this review is to present a small approach about “omics” technologies applied to the study of the effect of carbon nanomaterials in the cell.