We have previously demonstrated a modulation of Na+/H+ exchange (NHE) activity by vitamin D3 in the rat ileum and Caco-2 cells. However, the molecular mechanism(s) of action of vitamin D3 on NHE are still not understood. The current studies were undertaken to understand the regulation of individual NHE isoforms on mRNA levels in two distinct models of vitamin D3 deficiency. Acute D3 deficiency was induced secondary to streptozotocin-induced diabetes mellitus, while chronic D3 deficiency was induced by feeding a D3-deficient diet in an environment devoid of fluorescent light. Vitamin D3 deficiency in both models increased the initial rates of rat ileal brush-border membrane (BBM) Na+/H+ exchange by 2.5-fold compared to D-repleted controls. In parallel to the increased exchanger activity, NHE3 mRNA abundance was increased about twofold in both acute and chronic D deficiency compared to control. There was no change in NHE1 or NHE2 abundance in vitamin D3-deficient rat ileum. These findings indicate that vitamin D3 regulates Na+/H+ exchange activity in rat ileum by influencing the mRNA levels of NHE3, the predominant luminal membrane isoform involved in vectorial Na+ transport.