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Gastric varices are usually associated with a gastro-renal (G-R) shunt. However, the gastric varices described in this case report were not associated with a G-R shunt. The inflow vessel was the posterior gastric vein and the outflow vessels were the narrow inferior phrenic vein and the dilated cardio-phrenic vein. First, percutaneous transhepatic obliteration of the posterior gastric vein was performed, but the gastric varices remained patent. Then, micro-balloon catheterization of the subphrenic vein was carried out via the jugular vein, pericardial vein and cardio-phrenic vein, however, micro-balloon-occluded inferior phrenic venography followed by micro-coil embolization of the cardio-phrenic vein revealed no delineation of gastric varices resulting in no further treatment. Thereafter, as a gastro-subphrenic-intercostal vein shunt developed, a micro-balloon catheter was advanced to the gastric varices via the intercostal vein and balloon-occluded retrograde transvenous obliteration (BRTO) was performed resulting in the eradication of gastric varices. BRTO for gastric varices via the intercostal vein has not previously been documented.