We discuss a third-trimester diagnosis of Megacystis-microcolon-intestinal hypoperistalsis syndrome (MMIHS) using magnetic resonance imaging (MRI) and consider the benefits of MRI as a noninvasive imaging technique after routine ultrasonography reveals genitourinary pathology requiring further elucidation. MMIHS is a rare cause of functional gastrointestinal and genitourinary obstruction in newborns. Because of the poor prognosis of MMIHS, prenatal diagnosis is warranted for optimal prenatal counseling and postnatal treatment. Although MMIHS commonly presents on ultrasonography, the limitations of ultrasonography make definitive diagnosis difficult. However, MRI is safe, accurate, and can be used for early prenatal diagnoses of multisystem diseases.