KCC3 and KCC1 are potassium chloride transporters encoded by SLC12A6 and SLC12A4 with partially overlapping function, and KCC3 knockout mice exhibit hypertension. Two KCC3 isoforms differ by alternate promoters and first coding exons: KCC3a is widely expressed, and KCC3b is highly expressed in kidney proximal convoluted tubule. We genotyped KCC3 and KCC1 amino acid substitutions in 307 Suffolk, Rambouillet, Polypay, and Columbia sheep. Whole blood sodium and potassium concentrations were determined by atomic absorbance spectrometry. Association was determined by mixed models with breed and genotype for variant of interest as fixed effects, and sire nested within breed treated as random. No KCC3a or KCC1 substitutions were associated with blood potassium or sodium (all P>0.05). KCC3b R31I is a charged substitution located in a conserved motif and while not associated with potassium (P>0.05), it was associated with blood sodium in an underdominant manner where sodium was significantly higher in both homozygotes than in heterozygotes (P<=0.05). The sodium association is interesting because: 1) KCC3 is only known to transport potassium and chloride, not sodium, and 2) KCC3a interacts with the sodium-potassium pump, whereas KCC3b does not. Possible mechanisms include: A) R31I alteration of KCC3b sodium affinity, B) KCC3b oligomer formation with sodium transporters [7], or C) indirect influence, e.g. by impairing sodium-potassium pump efficiency through potassium availability. Regardless of specific mechanism, the underdominant pattern suggests allelic incompatibility such as dimer impairment. Since KCC3 functions as a homodimer, R31I may interfere with KCC3b dimer function in regulating sodium concentration. To our knowledge, this is the first report of a KCC3 variant associated with blood sodium. These data suggest further study of coordinated function between KCC3 and sodium transport, and sheep with KCC3b R31I may serve as a biomedical model.