Background: Partial ligation of the portal vein has been shown to induce not only prehepatic portal hypertension but also esophageal varices in the rat. We developed an esophageal endoscopic system for endoscopic sclerotherapy of esophageal varices in rats. In the present study the efficacy of three sclerosing agents, 1% polidocanol, 5% ethanolamine oleate, and 99.5% ethanol, was compared, using this model. Methods: Sclerosing agents were injected paravariceally in 42 rats with partial portal vein ligation. Their efficacy was compared endoscopically and histologically. Results: Ethanol induced the most severe ulcers and subsequent stricture formation. The damage induced by 1% polidocanol was mild and healed quickly, whereas 5% ethanolamine oleate induced moderate damage. The varices disappeared because of fibrosis that developed after ulceration. Conclusions: The results were consistent with the known properties of these three agents, suggesting that the esophageal endoscopic system for sclerotherapy in rats provides a useful method for experimental studies of sclerotherapy.