The occurrence of a cyst of the lesser vestibular gland is rare in neonates. It is a pathology secondary to a blockage of the duct’s opening in the area of labia minora. This is a report of a neonate case who presented on initial clinical examination with a membrane completely occluding the vaginal orifice. There were no other pathologies found on the examination. The initial diagnostics were performed on the Neonatology Ward. Subsequently the patient was referred to the Children and Adolescents Surgical and Urological Unit for further treatment. The incision of the cyst was performed. Ultrasonography is the preferred diagnostic modality in this kind of pathology. Differential diagnostic errors can lead to either unnecessary surgical interventions or delays in correct interventional treatment.