Purpose: To distinguish a metastasis from a second primary tumor in patients with a history of head and neck squamous cell carcinoma and subsequent pulmonary squamous cell carcinoma. Experimental Design: For 44 patients with a primary squamous cell carcinoma of the head and neck followed by a squamous cell carcinoma of the lung, clinical data, histology, and analysis of loss of heterozygosity (LOH) were used to differentiate metastases from second primary tumors. Results: Clinical evaluation suggested 38 patients with metastases and 6 with second primaries. We developed a novel interpretation strategy based on biological insight and on our observation that multiple LOH on different chromosome arms are not independent. LOH analysis indicated metastatic disease in 19 cases and second primary squamous cell carcinoma in 24 cases. In one case, LOH analysis was inconclusive. For 25 patients, LOH supported the clinical scoring, and in 18 cases, it did not.These18 discordant cases were all considered to be second primary tumors by LOH analysis. Conclusions: A considerable number of squamous cell lung lesions (50% in this study), clinically interpreted as metastases, are suggested to be second primaries by LOH analysis. For these patients, a surgical approach with curative intent may be justified.Patients treated for head and neck squamous cell carcinoma frequently develop second primary tumors in the lung (1 -3). Because the histologic appearance of the head and neck tumor and the lung lesion is similar (squamous cell carcinoma in both cases), the differential diagnosis between second primary or metastasis is mainly dependent on clinical criteria such as localization of the lung lesion, tumor stage, and disease-free interval. Warren and Gates (4) were the first to develop criteria for second primary tumors and additional studies have been published since (summarized in Table 1). The criteria employed, such as histology, tumor stage, and interval, however, do not give a definitive answer in the differential diagnosis mentioned above.Treatment options for patients with second primary lung tumors are different from those for metastasized head and neck squamous cell carcinoma. A resectable second primary would justify surgical approach with curative intent (5 -9), whereas metastatic disease would be treated with systemic therapy or limited surgical resection. Therefore, we looked for the identification of more objective markers in this differential diagnosis.In theory, clonal relationship between two tumors proves their common origin in case of metastases. Conversely, the absence of a clonal relationship would suggest a second primary carcinoma. Many assays have been developed to evaluate clonal relationship between tumors. Analysis of patterns of loss of heterozygosity (LOH) has been used to distinguish second primaries from metastases in the aerodigestive tract (10 -12). LOH analysis is easy to perform on paraffinembedded tissue and, thus, potentially very useful in everyday clinical practice, as well as for the ...