Broadly defined, nanoscale materials are substances in which at least one critical dimension is less than 100 nm. Nanoscale materials are employed in several industrial applications as well as in biology and medicine. Despite their wide use, very little research has been carried out on the potential toxicity of nanoparticles. For this reason, we report on a molecular approach in nanotoxicology research. Using the differential display technique, we focused our attention on mRNA expression in a BALB3T3 A31-1-1 cell line that was not exposed and exposed for 72 h to 1 microM of cobalt microparticles (Co-mu), nanoparticles (Co-nano), and ions. In the experiments, we obtained 10 differentially expressed sequences. These genes represent candidate biomarkers capable of indicating specific cellular effects after Co-nano exposure. In addition, our results show that treatment with Co-nano somehow activates cellular pathways of defense and repair mechanisms. It is also evident that molecular techniques are valuable tools in nanotoxicology research, where they will certainly find wide use.