Aquaporin-1 is the major protein responsible for transport of water across the epithelia of the proximal tubule and thin descending limbs. Rapid water efflux across the thin descending limb is required for the normal function of the countercurrent multiplier mechanism. Therefore urinary concentrating capacity is severely impaired in aquaporin-1 knockout (AQP1 -/-) mice. Here, we have investigated the long-term consequences of deletion of the aquaporin-1 gene product by profiling abundance changes in transporters expressed in the inner medullas of AQP1(-/-) mice versus heterozygotes [AQP1(+/-)], which have a normal concentrating capacity. Semiquantitative immunoblotting demonstrated marked suppression of two proteins strongly expressed in the inner medullary collecting duct (IMCD): UT-A1 (a urea transporter) and AQP4 (a basolateral water channel). Furthermore, the urea permeability of the IMCD was significantly reduced in AQP1(-/-) mice. In contrast, there was increased expression of three proteins normally expressed at higher levels in the cortical collecting duct (CCD) than in IMCD: AQP3 (another basolateral water channel) and the epithelial sodium channel subunits -ENaC and - ENaC. Changes in expression of these proteins were confirmed by immunocytochemistry. Messenger RNA profiling (real-time RT-PCR) revealed changes in UT-A1, -ENaC, -ENaC, and AQP3 transcript abundance that paralleled the changes in protein abundance. Thus, from the perspective of transport proteins, the IMCDs of AQP1 (-/-) mice have a significantly altered phenotype. To address whether these changes are specific to AQP1 (-/-) mice we profiled IMCD transporter expression in a second knockout model manifesting a concentrating defect, that of ClC-nK1, a chloride channel in the ascending thin limb important for urinary concentration. As in the AQP1 knockout mice, ClC-nK1 (-/-) mice showed decreased expression of UT-A1 and increased expression of -ENaC and -ENaC vs. WT controls. In conclusion, the expression profile of IMCD transporters is markedly altered in AQP1 -/- mice and this manifestation is related to the associated concentrating defect.