Proximal renal tubular acidosis (pRTA) results from an impairment of bicarbonate (HCO3-) reabsorption in the renal proximal tubules, characterized by a decreased HCO3- threshold. pRTA commonly occurs as a manifestation of a generalized functional defect in proximal tubules. In contrast, pRTA can occur without other functional defects in proximal tubules (isolated pRTA). Most of the isolated pRTA in children are hereditary. Recent progress in molecular biological analyses is unraveling the molecular basis of hereditary pRTA. Mutations in the kidney type Na+/HCO3- cotransporter gene (SLC4A4) cause permanent isolated proximal RTA with ocular abnormalities. Mutations in carbonic anhydrase II gene lead to osteopetrosis, RTA (pRTA, distal RTA or combined proximal and distal RTA), cerebral calcification, and mental retardation. SLC9A3, encoding the Na+/H+ exchanger, is a candidate gene for pRTA without other manifestations. These results help further understand the molecular basis of hereditary pRTA and characterize the clinical and genetic manifestations of the disorder.