Comparative genomic hybridization (CGH) was used to detect chromosomal changes during metastasis formation of head and neck squamous cell carcinomas (HNSCCs). In total, 92 tumors of 54 patients were investigated. In 34 of these, the metastases were compared to the corresponding primary tumors. The group of metastatic tumors was also compared with 20 nonmetastatic tumors. Gain of 3q was the earliest genetic marker for invasion and metastasis and also correlated with poor prognosis. Additional metastasis-associated lesions were gains on 11q13, 7q11.2, 1q21-q22, and losses on 8p, 11p14, 11q14-qter, 10p12, 10q, and 14q. The incidence of the chromosomal changes was used to evaluate their significance and temporal order of appearance during tumor dissemination, thus leading to an extended progression model of HNSCC. In the clonality analysis, three different methods revealed a mean concordance of 64 and 68% between pairs of primaries and metastases, respectively. Using different similarity scores, the correct metastasis was identified from the pool of all metastatic lesions in 19-26 of the 34 cases. The study supplements previous genetic results on HNSCC pathogenesis and provides criteria for multiple tumor analysis.