The cyanobacterial hepatotoxin microcystin-LR (MC-LR) is a specific potent PP1 and PP2A protein phosphatase inhibitor. In view to obtain an integrated whole-body, understanding of the key target organs of MC-LR subsequent to embryonic exposure on the anatomy of medaka fish hatchlings, embryos at stage 19 were microinjected with a sublethal dose of MC-LR corresponding to 0.2 pg/vitellus. MC-LR-induced histo-pathological modifications of the alimentary system (i.e. digestive tract, pancreas, liver) were analysed in newly hatched embryos. Our data are indicative of an MC-LR-induced inhibition of both yolk sac resorption and gas concentrating swimbladder expansion. In contrast to control hatchlings, (i) no mucus-secreting cells in the oesophagus, (ii) a decreased folding of the stomach and intestine, (iii) a clear reduction in size of the exocrine pancreas associated with a destructuration of acinar units, and (iv) a strong decrease in the mass and size of the liver were observed in MC-LR treated embryos. Furthermore, as an indication of MC-LR-induced hepatic glycogen store depletion, unstained cytoplasmic areas present in control hatchling hepatocytes, were fully absent in all liver examined in treated embryos. Finally, as a general observation in MC-LR-treated embryos, our data clearly indicated terminal differentiation disorders in all organs associated with the digestive tract.