Müllerian agenesis (Mayer-Rokitansky-Küster-Hauser syndrome) is typically described as missing uterus and fallopian tubes with malformation of the upper vagina. Isolated uterine anomaly is a rare variant of the syndrome. A 16-year-old female with primary amenorrhea and rudimentary uterus on the magnetic resonance imaging (MRI) was reported. The ovaries, vaginal canal and other abdominal and pelvic organs were normal. The patient's sexual, physical and developmental characteristics were normal. The serum follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol, prolactin, testosterone and thyroid-stimulating hormone (TSH) were also normal. Thus, this patient represents an important variant of the Müllerian agenesis syndrome.