We report a case of gastrointestinal stromal tumor (GIST) with liver metastases which was undetectable by B-mode ultrasonography, effectively treated by radiofrequency ablation using contrast-enhanced ultrasonography US. A 43-year-old woman was admitted for the treatment of 6 lesions up to 4cm in diameter, which had emerged from necrotic sites within the liver after imatinib treatment. The recurrent lesions were not detected on B-mode US, and it was difficult to perform radiofrequency ablation (RFA) treatment. Using a contrast-enhanced agent (sonazoid), the recurrent lesions were detected and treated by RFA. RFA is considered to be an effective treatment for GIST with liver metastases that tolerate imatinib administration.