Due to their unique physical and chemical properties, gold nanoparticles (AuNPs) are promising in a wide variety of biomedical applications. However, there are several indications that AuNPs may be toxic and that particle size is an important factor. The immune system plays a key role in the biological response to nanoparticles and inflammation has been commonly associated with nanoparticle induced toxicity. The main objective of this study was therefore to investigate the inflammatory potential of three different sizes of AuNPs, in vivo, using the zebrafish embryo model. Briefly, zebrafish embryos were injected intravascularly with sub-lethal doses (0.1, 0.5 or 1.0 µg/mL) of 20, 40 or 80 nm citrate stabilized AuNPs at 72h post fertilization (hpf). Three replicates of the injected and the control fish were collected at 2, 24 and 48 h post injection (hpi) and the expression of proinflammatory (tnfa, il1b, il8, il12a and ifng) and anti-inflammatory (il10) genes related to the innate immune system were measured by reverse transcription-quantitative PCR (RT-qPCR). Survival studies in zebrafish were conducted prior to the immune response assessment to determine a sub-lethal dose range, and revealed only moderate effects on survival following exposure to 80 nm AuNPs. Results from the gene expression analysis showed an increased transcription of all the inflammatory genes, primarily at 2 hpi, which subsided to control levels by 48 hpi. The transcription of the proinflammatory cytokines TNF-α, IL-1β and IFNγ was considerably lower for 20 nm AuNPs and might reflect differences related to particle size. The observed effects did not seem to be highly correlated with the injected dose, although there was a tendency for the highest doses to elicit the highest response. Overall, this study suggests that the examined AuNPs induce a transient, inflammatory response in zebrafish.