The occurrence of Müllerian anomalies with concomitant gonadal abnormalities is very rare. The most common cause of primary amenorrhea is gonadal dysgenesis and Mullerian agenesis. Here we report two young females who presented with primary amenorrhea, poorly developed secondary sexual characteristics and short stature. In both cases, breasts weren’t developed yet with absent pubic hair and normal appearing female external genitalia. The hormone analysis revealed elevated level of follicle-stimulating hormone and luteinizing hormone which pelvis MRI indicated uterine and vaginal dysplasia with absent ovaries in both cases. Karyotyping may help in differentiating the diagnosis. Treatment options and breaking the bad news was difficult in both cases as surrogacy or assisted fertility wasn’t convincing in these cases.