Objective To develop imaging guidelines for the MR work-up of female genital tract congenital anomalies (FGTCA). Methods These guidelines were prepared based on a questionnaire sent to all members of the European Society of Urogenital Radiology (ESUR) Female Pelvic Imaging Working Group (FPI-WG), critical review of the literature and expert consensus decision. Results The returned questionnaires from 17 different institutions have shown reasonable homogeneity of practice. Recommendations with focus on patient preparation and MR protocol are proposed, as these are key to optimised examinations. Details on MR sequences and planning of uterus-orientated sequences are provided. Conclusions The multiplanar capabilities and soft tissue resolution of MRI provide superb characterisation of the wide spectrum of findings in FGTCA. A standardised imaging protocol and method of reporting ensures that the salient features are recognised, contributing to a correct diagnosis and classification of FGTCA, associated anomalies and complications. These imaging guidelines are based on current practice among expert radiologists in the field and incorporate up to date information regarding MR protocols and essentials of recently published classification systems. Key Points • MRI allows comprehensive evaluation of female genital tract congenital anomalies, in a single examination. • A dedicated MRI protocol comprises uterus-orientated sequences and vaginal and renal evaluation. • Integration of classification systems and structured reporting helps in successful communication of the imaging findings.