Calcineurin inhibitors like FK506 (Tacrolimus) are routinely used for immunosuppression following transplantation. Its use is limited by many side effects including renal tubular acidosis (RTA), mainly of the distal type. In this study, rats were treated with FK506 and at baseline (after 9 days) systemic acid base status was similar to control animals. However, FK506 treated rats given NH₄Cl in the drinking water for 2 days developed a more severe metabolic acidosis than control animals. Despite the more pronounced acidosis in the FK506 treated rats, urine pH was more alkaline, indicative of RTA. After 7 days acid load all differences related to acid-base homeostasis were equalized in both groups. Protein abundance of NaPi-IIa, NHE3, kNBCe1, and both a4 and B2 subunits of the vacuolar H⁺-ATPase were reduced under baseline conditions, while induction of metabolic acidosis enhanced protein abundance of these transporters in FK506 treated animals. In parallel, protein expression of AE1 was reduced at baseline and increased together with pendrin during NH₄Cl loading. Protein abundance of the Na⁺- bicarbonate cotransporter NBCn1 was reduced under baseline conditions but remained downregulated during metabolic acidosis. Morphological analysis revealed an increase of the relative number of non-type A intercalated cells in the connecting tubule and cortical collecting duct at the expense of principal cells. Additionally, subcellular distribution of the a4 subunit of the vacuolar H⁺-ATPase was affected by FK506 with less luminal localization in the CNT and OMCD. These data suggest that FK506 impacts on several major acid base transport proteins in the kidney and its use is associated with transient metabolic acidosis and altered expression of key renal acid-base transport proteins.