The frequency of the dominant model (TG/TT) of rs34072914 in WNT9B was significantly increased in the women with MRKH syndrome compared with the controls (P = 0.039, OR = 2.47, 95%CI = 1.02–5.96), and this result was consistently observed in the women with MRKH type II (P = 0.027, OR = 4.78, 95%CI = 1.34–17.11). Here, WNT9B is linked to Mayer-Rokitansky-Küster-Hauser syndrome.