Congenital abnormalities of the kidney and urinary tract include a wide range of malformations ranging from asymptomatic to life-threatening conditions. Although pediatric urogenital system imaging is based on the use of US (pre-and postnatal), voiding cystourethrography and scintigraphic study, magnetic resonance (MR) urography plays a fundamental role in the classification and management of congenital abnormalities of the kidney and urinary tract, giving an overview of the different clinical pictures, thanks to its panoramicity and high anatomical detail. In fact the anomalies of the urinary tract are phenotypically variable because they can affect simultaneously several segments of different embryonic derivation, with complex clinical pictures; they can appear both as isolated phenotypes or as complex malformative conditions, involving renal parenchyma, collecting system and bladder. A deep knowledge of this complex embryogenesis and its possible phenotypic patterns allows a correct interpretation of MR urography images. We describe the embryology and pathophysiology of congenital abnormalities of the kidney and urinary tract as well as MR urography technique and findings. Congenital abnormalities of the kidney and urinary tract are classified into four groups: (1) obstruction (proximal, middle and distal), (2) budding with respect to the Wolffian duct (site and number of ureter), (3) ascent and rotation (ectopia, malrotation and fusion of kidney) and (4) anomaly of metanephric differentiation (dysplasia, megapolicalycosis).