Transabdominal ultrasound (US) has not proved completely reliable in Müllerian duct anomalies. One study has shown it useful in obstructed uterovaginal anomalies. We are unaware of a study that has used endovaginal ultrasound in children to investigate uterovaginal anomalies. Magnetic resonance imaging (MRI) is now gaining wide acceptance in imaging congenital abnormalities of the genital tract. To identify the problems and potential pitfalls of using MRI to evaluate the female genital tract in paediatric patients. A retrospective review of the MRI scans of 19 patients, aged 3 months to 19 years (mean 14 years), with uterovaginal anomalies. The uterovaginal anomalies were categorised into three groups: (1) congenital absence of the Müllerian ducts, or the Mayer-Rokitansky-Kuster-Hauser syndrome (n = 7), (2) disorders of vertical fusion (n = 2) and (3) disorders of lateral fusion (n = 10). MRI is a reliable method for evaluating paediatric uterovaginal anomalies, but should be analysed in conjunction with other imaging modalities (US and genitography). Previous surgery makes interpretation more difficult and, if possible, MRI should be carried out prior to any surgery. An accurate MRI examination can be extremely helpful prior to surgery and it is important for the radiologist to have knowledge of how these complex anomalies are managed and what pitfalls to avoid.