This study gives a three-dimensional (3D) structural analysis of rat nephrons and their connections to collecting ducts. A total of 4500, 2.5-µm-thick serial sections from the renal surface to the papillary tip were obtained from three kidneys of Wistar rats. Digital images were recorded and aligned into three image stacks and traced from image to image. Short-loop nephrons (SLNs), long-loop nephrons (LLNs), and collecting ducts (CDs) were reconstructed in 3D. We identified a well-defined boundary between the outer stripe and the inner stripe of the outer medulla corresponding to the transition of descending thick limbs to descending thin limbs and between the inner stripe and the inner medulla, i.e. the transition of ascending thin limbs into ascending thick limbs of LLNs. In all nephrons a mosaic pattern of proximal tubule (PT) cells and descending thin limb (DTL) cells was observed at the transition between the PT and the DTL. The course of the LLNs revealed tortuous proximal "straight" tubules and winding of the DTLs within the outer half of the inner stripe. The localization of loop bends of SLNs in the inner stripe of the outer medulla and the bends of LLNs in the inner medulla reflected the localization of their glomeruli, i.e. the deeper the glomerulus, the deeper the bend. Each collecting duct drained approximately 3 to 6 nephrons with a different pattern than previously established in mice. This information will provide basis for evaluation of structural changes within nephrons as a result of physiological or pharmaceutical intervention.