We previously reported that in rats, long-term Zn deficiency significantly reduced taste sensitivity and total carbonic anhydrase (CA) activity in the submandibular gland. We therefore investigated the effects of Zn deficiency on salivary secretion and the expressions of CA isozymes (II and VI) in the rat submandibular gland, since those isozymes are thought to be related to taste sensation and salivary secretion. Male Sprague–Dawley rats, age 4 weeks, were divided into three groups (Zn-def, low-Zn and pair-fed, that were fed a diet containing 2·2, 4·1 or 33·7 mg Zn/kg, respectively, for 42 d). Northern blot analysis indicated that Zn deficiency reduced CA II mRNA expression in the submandibular gland without reducing CA VI mRNA expression. In Western blot analysis, Zn deficiency significantly reduced CA II (erythrocyte CA) protein expression in the submandibular gland without reducing CA VI protein expression. Salivary secretion was lower in the Zn-def group than in the pair-fed group. These results suggest that decreased CA isozyme II expression underlies the decreased CA activity previously reported in the submandibular gland in Zn-def rats, and this may reduce regular salivary secretion.