We report on the association of Mayer-von Rokitansky-Küster-Hauser syndrome (MRKHS) with a unique form of Holt-Oram syndrome (HOS) with an aorto-pulmonary window. A 24-year-old Turkish woman was referred to our hospital because of primary amenorrhoea. Both her vagina and uterus were absent, and the diagnosis of MRKHS was established. Laparoscopic creation of a neovagina by the modified Vecchietti technique was performed. A rare congenital malformation of the heart, namely an aorto-pulmonary window, had required cardiac surgery when the patient was a 6-month-old infant. This cardiac malformation plus associated upper limb anomalies led to the clinical diagnosis of HOS. To the best of our knowledge, this is only the second report in the scientific literature on the concurrence of MRKHS and HOS, and the first published case of HOS with an aorto-pulmonary window as the cardiac malformation.