Nephrons are tiny tubules (miniature tubes) which make up the smallest working part of the kidney. In other words, they are the smallest level where the kidney removes waste, excess salt and excess water. Each nephron starts in the cortex of the kidney, then goes into the medulla of the kidney, before coming back to the cortex, then goes through the medulla into the pelvis. In the pelvis, the nephrons join up with the ureter.