Previous studies have demonstrated that a missense single-nucleotide polymorphism variant (2316A>G; rs2230739) of the adenylate cyclase type IX gene was associated with bipolar disorder and affective disorder. We determined genotype and allele frequencies using a ligase detection reaction method in 315 patients with major depressive disorder and 278 unrelated, sex-matched healthy control subjects. We did not detect any statistically significant differences in genotype and allele frequencies between patients and healthy control subjects. Furthermore, we found no significant difference between genders in major depressive disorder, nor between patients and controls in the same gender. These results suggest that 2316A>G (rs2230739) may not be a risk factor for increasing susceptibility to major depressive disorder in the Chinese Han population.