Recent autopsy studies have clarified the frequency of lymph node (LN) metastases from hepatocellular carcinoma (HCC). However, LN metastases commonly occur in advanced and poorly differentiated HCC and are very rare in small HCC. We encountered a patient with skip LN metastases from a small HCC, 10 mm in diameter. An intra-abdominal tumor adjoining the duodenum was detected by follow-up ultrasonography for viral hepatitis C. Computed tomography showed, in addition to the tumor bordering the duodenum, a small low-density area of the liver (S6), 2 cm in diameter, and a swelling of LN adjacent to the common hepatic artery. Upper gastrointestinal rentogenography revealed a compression of the duodenal second portion without irregularity of the mucosa. Our pre-operative diagnosis was duodenal gastrointestinal stromal tumor with LN metastasis and HCC or liver metastasis. However, laparotomy proved them to be LN metastases from a small HCC and partial hepatectomy and LN dissection were performed. The patient is doing well 22 months after surgery with no signs of recurrence. In the cases of HCC with LN metastases, the prognosis is generally very poor. However, in small HCC, the clinical characteristics are not fully evaluated. In treatment, we have to keep LN metastases, particularly skip LN metastases, in mind, even in cases of small HCC.