BACKGROUND: Primary care physicians are frequently faced with the challenge of evaluating primary amenorrhea in adolescent girls. Approximately 15% of these women have abnormal genital examination, with Müllerian agenesis being the second most frequent cause. We report two cases of adolescents with Müllerian agenesis that presented to a tertiary adolescent medicine center with primary amenorrhea and the very rare sexual phenomenon of urethral coitus. The aim of this report is to emphasize the importance of performing a genital examination in girls who present with amenorrhea in the primary care setting, even if 'normal' vaginal sexual activity is assumed.CASE PRESENTATIONS: A 19-year-old Caucasian and a 16-year-old Filipino girl presented to a tertiary adolescent medicine center with primary amenorrhea and a history of 'normal' vaginal coitus. Investigation revealed Müllerian agenesis in association with urethral coitus in both cases; neither patient suffered significant urethral damage to require urethra reconstruction. However, the first adolescent had recurrent pyelonephritis and renal scarring and the second had dysuria.To the best of our knowledge, Case 1 also represents the second reported case of pituitary prolactinoma in association with Müllerian agenesis. The first adolescent underwent a hernia repair and vaginoplasty, whereas the second had vaginal dilatations.CONCLUSION: Our cases highlight the need for careful assessment of the external genitalia and vagina patency in all girls with amenorrhea, even if they report 'normal' vaginal sexual activity. Early identification of anatomic disorders such as Müllerian agenesis, will allow provision of proper care according to the patient's needs and the existing abnormalities, and prevention of rare, unintentional but potentially physically and emotionally harmful, patterns of sexual intercourse.