Background Magnetic resonance imaging (MRI) of the pelvic floor allows better assessment of pelvic pathology and has a potential as an adjunct for therapy planning. In complex congenital malformations of the pelvic floor and continence organs, it plays a major role in assessing urinary and fecal incontinence or constipation, especially when performed as a dynamic investigation such as MRI defecography. Patients and Methods Twenty-three patients (3-21 years old) with urinary and/or fecal incontinence or constipation attributable to congenital malformations of the pelvic region presented at our institution. The diagnoses were anorectal malformations (18), bladder exstrophy (2), and cloacal exstrophy (3). All patients underwent static and dynamic MRI of the pelvic floor with rest, squeeze, and evacuation in supine position. Results Morphology and function of the pelvic floor and pelvic organs could be demonstrated in each case. The reason for urinary incontinence, fecal incontinence, or constipation could be defined, and an individual therapeutic management concept was made based upon the data obtained by the investigation. Conclusions The advantages of this method, in comparison to others, are direct visualization of the pelvic floor muscles and continence organs and their anatomical relationship during different functional actions. Pelvic floor dysfunction is often the reason for fecal and urinary incontinence and can be detected by MRI. Especially in children, minimizing radiation exposure is of major concern. Disadvantages are the costs and long investigation time.