Three different types of vaginal outlet obstruction are described in the literature: imperforate, transversal vaginal septum and vaginal atresia. Diagnoses were made in different ages of life, from neonatal to the teenage years. Clinical and ultrasound examinations and MRI dominated in establishing the diagnosis. Complex malformations of female genital tract are not so common.Their correct identification is of paramount importance for appropriate management. A thorough knowledge of embryology, pre-operative imaging with MRI and examination under anaesthesia is essential to identify accurately the constellation of anomalies and to plan appropriate management. This case reports distal vaginal agenesis in an 13 year old girl which was managed by dissecting the lower half of vagina and pull-through vaginoplasty. Rarity and variable presentation of congenital genital tract anomalies can lead to delayed diagnosis and erroneous management. A high index of suspicion and cross-sectional imaging can help in early diagnosis. A comprehensive management is imperative to preserve the reproductive potentials, as significant proportion of patients may experience sexual difficulties, menstrual irregularity, and infertility.