Transcatheter arterial embolization therapies (TAE) for multiple hepatocellular carcinomas (HCCs) were performed repeatedly, but had no effects on one or two of the tumors because of the development of collateral arteries. We report a case of which one of the tumors fed by collaterals showed good anti-cancer effects by microwave coagulation therapy (MCT) under mini-thoracotomy. The 70-year-old, male patient with HCC underwent two hepatic resections and one TAE before this admission. On the arteriogram, one of the tumors existing in S6, which was 2 cm in size, was supplied by the right 10th intercostal artery. We carried out MCT under mini-thoracotomy for the tumor in S6 two weeks after conventional hepatic embolization. First, two MCTs using a long electrode, 3 cm in size, were performed in the central area of the tumor, and eight MCTs by a short electrode, 2 cm in size, were done in the peripheral and surrounding area of the tumor. He was discharged 16 days after the therapy without any serious complications. On CT 3.5 months after therapy, no local recurrence of the tumor was recognized. MCT under mini-thoracotomy is a low-invasive, safe and effective therapeutic method for small HCC fed by collaterals.