The increasing use of nanotechnology in the last decade has raised concerns about the impact of nanoparticles in the environment. In particular, the potential harmful effects of iron oxide nanoparticles (IONPs) in aquatic organisms have been poorly addressed. We analyze here the toxic effects induced by IONPs in zebrafish using a combination of classical (genotoxicity, oxidative stress) and molecular (transcriptomic) methodologies. Adult animals were exposed for 96h to five sub-lethal IONP concentrations, ranging from 4.7 to 74.4mg/L. Comet and micronucleus assays revealed a significant number of DNA lesions induced by IONPs at all concentrations tested. Conversely, the thiobarbituric acid reactive substances (TBARS) test detected only a mild oxidative damage in liver cells (∼1.5-fold increase of malondialdehyde concentrations) and only at the two higher IONP concentrations tested. Microarray analysis of liver samples identified 953 transcripts (927 unique genes) differentially expressed between controls and IONP-exposed samples. Subsequent functional analysis identified genes related to cation/metal ion binding, membrane formation, and morphogenesis among the transcripts overrepresented upon IONP treatments, whereas mRNAs encompassing genes associated with RNA biogenesis, translation, ribosomes, and several metabolic processes became underrepresented in treated samples. Taken together, these results indicate considerable genotoxic effects of IONPs combined with general negative effect on cell growth and on the ability of the cell produce new proteins. On the contrary, IONPs showed only a limited capacity to induce oxidative stress. To our knowledge, this is the first study on IONPs toxicity using such an integrative approach in an aquatic organism.