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Mayer–Rokitansky–Küster–Hauser (MRKH) syndrome is a rare congenital female genital anomaly, which is caused by aplasia of the caudalportion of the Müllerian duct. The WNT9B gene encodes a secretory glycoprotein essential for the caudal extension of the Müllerian duct during embryonic development in mice. Coding regions and exon/intron boundaries of the WNT9B gene were amplified and sequenced in 42 Chinese women with MRKH syndrome and 42 controls. Two novel heterozygous mutationswere identified,which were absent in controls. Onewas amissensemutation in exon 1, and the other was located in the 30-untranslated region. Both variants were detected in one out of 42 patients. The two novel mutations may be pathogenic variants in MRKH patients and warrant further functional study.