Three-dimensional functional reconstructions of descending thin limbs (DTLs) and ascending thin limbs (ATLs) of Henle’s loops, descending vasa recta (DVR), ascending vasa recta (AVR), and collecting ducts (CDs) permit quantitative definition of lateral and axial zones of probable functional significance in rat inner medulla (IM). CD clusters form organizing motif for Henle’s loops and vasa recta in initial 3.0-3.5 mm of IM. Using Euclidean distance mapping, we defined lateral boundary of each cluster by pixels lying maximally distant from any CD. DTLs and DVR lie almost precisely on this independently defined boundary, placing them in intercluster interstitium maximally distant from any CD. ATLs and AVR lie in nearly uniform pattern throughout both intercluster and intracluster regions, which we further differentiated by a polygon around CDs in each cluster. Loops associated with individual CD clusters show similar axial exponential decrease as all loops together in IM. Because ~3.0-3.5 mm below IM base CD clusters cease to form organizing motif, all DTLs lack aquaporin 1 (AQP1), and all vasa recta are fenestrated, we have designated first 3.0-3.5 mm of IM as "outer zone" (OZ) and final 1.5-2.0 mm as "inner zone" (IZ). We further subdivided these into OZ1, OZ2, IZ1, and IZ2, based on presence of completely AQP1-null DTLs only in first 1 mm and on broad transverse loop bends only in final 0.5 mm. These transverse segments expand surface area for probable NaCl efflux around loop bends from ~40% to ~140% of CD surface area in final 100 µm of papilla.