The substance of the kidney is made up of an outer cortex and an inner medulla. A portion of each nephron may be located in both cortex and medulla, but the renal corpuscles are only present in the cortex. The cortex can be divided into an outer zone and inner zone based on the distribution of the corpuscles. The medullary rays are groups of straight collecting tubules and loops of Henle in the cortex. Between the medullary rays are cortical labyrinths, composed of renal corpuscles and convoluted tubules.

According to the combination of renal tubules at different areas, the medulla may also be divided into an outer zone and inner zone. The outer zone is further subdivided into an outer stripe and inner stripe.

The medulla is arranged into 10-18 pyramidal structures, known as renal pyramids. The base and sides of the renal pyramids are within the cortex, and their vertices, the renal papilla, protrude into the minor calyx. The renal pyramids are separated by a layer of connective tissue and the renal column, which possesses cortical structure. One renal pyramid is also called a lobe. A renal lobule is composed of a single medullary ray and the cortical tissue surrounding it.