Urinary stone formation is closely associated with abnormal excretion and secretion of organic anions, including uric acid and dicarboxylates such as oxalate and citrate. Hyperuricemia contributes to stone formation by increasing urinary uric acid concentrations, and urinary stones are frequently observed in patients with gout. Urinary levels of these organic acids are primarily determined by transporters expressed in renal proximal tubules. In this review, we provide an overview of key organic anion transporters (OAT1, OAT3, and OAT4), which mediate the exchange of organic anions driven by intracellular dicarboxylates. These dicarboxylates are supplied by Na+-dependent dicarboxylate cotransporters, such as NaDC1 and NaDC3. Additionally, we describe other relevant transporters, including CFEX and Sat-1, which are involved in the transport of oxalate, a key factor in calcium stone formation. Urinary stones are considered to result from imbalances in the reabsorption and secretion of various compounds, including organic anions, regulated by renal tubular transporters. Further investigation of such transport mechanisms may contribute to the development of novel therapeutic strategies targeting these transporters.