The Mayer–Rokitansky–Kuster–Hauser syndrome (MRKH syndrome), also called Rokitansky syndrome or vaginal aplasia of the uterus, is a congenital condition characterized by the absence of the uterus and vagina, however, ovaries are present and the external genitalia are normal. There are two different forms of this syndrome: typical and atypical form. We report a case of atypical form of MRKH syndrome in a 15year old female who presented with primary amenorrhoea. On examination, blind vagina noted and uterus not palpable per rectally. On sonographic evaluation, Uterus was not visualized. Bilateral renal fossa are empty with ectopic right kidney. On MRI, Post contrast studies showed rudimentary uterine tissue and right ectopic kidney is noted in pelvis. Karyotyping revealed 46XX. MRKH atypical form should be in mind if there are features of its history, physical examination, US and MRI evaluations in a patient with primary amenorrhea.