Abstract Background: Cyanobacterial toxic blooms often occur in freshwater lakes and constitute a potential health risk to human population, as well as to fish community or other aquatic organisms. Microcystin-LR (MC-LR, the most commonly detected cyanotoxin in the freshwater environment) is a potent hepatotoxin, deregulating kinase pathway via phosphatases 1 and 2A inhibition. Although toxicological effects have been clearly related to the in vitro exposure of fish to purified microcystins, cyanotoxins are produced by the cyanobacteria together with numerous other potentially toxic molecules, and their global and specific implications on the health of fish are still not clearly established and remain puzzling to assess. Methods: Medaka fish (Oryzias latipes) was chosen as an in-vitro model for studying the effects of a cyanobacterial bloom on liver protein contents using a gel-free quantitative approach, iTRAQ, in addition to anatomic-pathological investigations. Fish were gavaged with cyanobacterial extracts (Planktothrix agardhii) from a natural bloom (Lake of La Grande Paroisse, France) containing 2.5 ?g eq. MC-LR per 5 ?l. Two hours after exposure, fish were sacrificed and organs were collected for analysis. Results: Using proteomic approach, 304 proteins could be identified in treated fish livers, 147 presenting high confidence identification, among which 15 revealed statistically significant variations in comparison with controls (gavaged with water only). Overall, these protein regulations clearly testify to the occurrence of oxidative stress and lipid regulation effects in the liver of medaka fish. Differently to pure mycrocystin-LR gavage experiments, a strong induction of Vitellogenin1 protein was observed for the first time with a cyanobacterial extract. This result was confirmed by ELISA quantification of vitellogenin liver content. Conclusions: These results suggest the occurrence of an endocrine disruptor effect of estrogen-type of the Planktothrix bloom extract, whether this reproductive effect can be attributed to microcystins need further investigation.