Follow-up protocols in patients after complete resection of high-risk cutaneous tumors lead to a discovery of metastases in very early stages, but surgery on non-palpable lesions proves to be challenging. In this monocenter retrospective study 39 patients suffering from malignant skin tumors with suspicious non-palpable lesions located in the lymph nodes (90%) or deep subcutaneously/intramuscularly (10%) were included. In 21 patients the lesions were excised under ultrasound guidance, and 18 patients received a wire marking before surgery. Both patient groups were compared regarding successful intraoperative finding of the lesion, duration of the procedure, and complications. Wire marking led to a significantly higher intraoperative detection rate of 100% versus 76% (p<0.05). The average time needed for the complete procedure (p = 0.91) or the rate of complications (p = 0.70) did not differ significantly between both groups. The size of the malignant lesions successfully removed by wire marking was significantly smaller (p<0.05). Of all 34 detected lesions only 20 (58.8%) were confirmed to be malignant. Wire marking increases the detection rate of non-palpable suspicious subcutaneous or lymphatic lesions. It leads to earlier diagnosis of metastasis but also allows to avoid unnecessary complete lymph node dissection.