The intestine of the fish, together with the gills, is an important organ in the uptake of heavy metals. Using histopathology, this study aimed to investigate the effects of two heavy metals (copper and zinc) on the intestine of Acipenser stellatus juveniles. Intestinal samples from stellate sturgeon were fixed in 10% formalin for 24h. The specimens were processed through paraffin embedding and 7 micrometer sections were cut, stained by Hematoxylin and Eosin and observed under light microscope. Exposure to heavy metals had significant effects on the histological organization of the intestine. The results of the present study showed that heavy metals exert their toxic effects on different intestinal layers, most of the lesions being observed on the intestinal mucosa. Of the two metals, copper induced major histopathological changes in the intestinal mucosa, compared to zinc.