ADPKD is associated with renal tubular acidosis. The aim of this study was to investigate the molecular mechanisms of metabolic acidosis in ADPKD and elucidate key acid-base transport proteins involved. We used an animal model for ADPKD (Han:SPRD rat (Cy/+)) and wild type rats served as controls. All animals were treated at baseline with standard diet and consecutively challenged with HCl diet for 2 days to induce metabolic acidosis. Under baseline conditions, both groups showed similar arterial blood pH but lower HCO₃^- and pCO₂ in ADPKD rats. After 2 days HCl diet, ADPKD animals showed a much more severe metabolic acidosis when compared to controls. At baseline, urinary pH was significantly lower in Cy/+ rats. However, after an acid load with HCl, control and ADPKD rats acidified their urine to the same pH indicating preserved ability to acidify urine. Urinary ammonium excretion was much lower in Cy/+ rats compared to controls. Using realtime RT-qPCR, the kidney specific phosphate transporters NaPi-IIa and NaPi-IIc were significantly down-regulated whereas Pit-2 was up-regulated in Cy/+ rats. Also, relative mRNA abundance of the Na⁺/H⁺ exchanger NHE3 and the Cl^-/HCO₃^- exchanger AE1, as well as the glutamine transporter SNAT3 were reduced. Immunoblotting for NaPi-IIa, NaPi-IIc, NHE3 and AE1 showed down-regulation in Cy/+ rats. In conclusion, cyst formation in Han:SPRD rat model causes renal acidosis and results in more severe metabolic acidosis upon acid-loading. Cy/+ rats showed normal urinary acidification but reduced expression of key transport proteins involved in ammoniagenesis and bicarbonate regeneration.