The occurrence of runt sturgeons is not an unusual event in rearing Acipenser transmontanus. The aim of this study was to describe morphological and histochemical features of the alimentary canal in both feeding and runt fish in order to identify specific structural changes that characterize the differences resulting from the nutritional status of the fish. Compared to feeding fish, runt fish showed: (i) a lack of lobuli of adipose tissue in the tunica propria-submucosa of their oesophagus; (ii) an increased thickness of the intestine near the spiral valve, due to the presence of several large lymphatic follicles within the tunica propria-submucosa; (iii) a reduced height of the intestinal folds; and (iv) a lesser immunohisto-chemical reactivity of the intestinal mucous cells towards a macrophage antiserum. The results tentatively suggest that a reduced defensive mucosal effectiveness occurs in runt specimens and this may be either linked to specific environmental stressors or to responses caused by pre-exposure to so far undetected disease agents, which requires further studies.