BACKGROUND: Baseline staging is important in all melanoma types, including melanoma with unknown primary site (MUP). Staging includes different examination strategies, each with different accuracy. OBJECTIVE: To determine the value of serum S100 protein levels and positron emission tomography (PET) in the baseline staging of MUP. METHODS: Twenty patients with MUP were evaluable for the analysis between 1996 and 2007 with both S100 assessment and PET performed for baseline staging. RESULTS: Serum S100 was elevated in 7 patients (35%). The PET scan detected the metastases in 6 of 7 patients with elevated serum S100 protein showing a strong correlation (p = 0.005). Patients with metastases had significantly higher serum S100 levels (p = 0.01) than the ones without. Serum S100 protein was shown to be discriminative between patients with and without metastases (receiver-operating characteristic, p = 0.012) with 75% sensitivity and 92% specificity. CONCLUSION: Serum S100 protein appears to be a sensitive as well as specific marker to detect metastases. We therefore might recommend serum S100 assessment to be included in the baseline staging of MUP.