The impact of a daily ration of food containing gold nanoparticles (AuNPs) of two sizes (12 and 50 nm) was investigated in the zebrafish Danio rerio at very low doses (from 36–106 ng gold/fish/day). AuNP exposure resulted in various dysfunctions at the sub cellular scale, and AuNP concentration in food, AuNP size and exposure duration modulated the observed adverse effects. Indeed, we showed alteration of genome composition using a RAPD-PCR genotoxicity test as the number of hybridization sites of the RAPD probes was significantly modified after AuNP exposure. Moreover, the expression of genes involved in DNA repair, detoxification processes, apoptosis, mitochondrial metabolism and oxidative stress was also modulated in response to AuNP contamination. Mitochondrial dysfunctions appeared in brain and muscle for both tested doses (40 and 100 ng gold/fish/day), but gold accumulation in fish tissues could only be observed in the case of the highest exposure dose.