In an attempt to define chromosomal alterations that are associated with the metastatic phenotype, we investigated a total of 29 metastasizing (pN+) and 19 non-metastasizing (pN0) head and neck squamous cell carcinomas by comparative genomic hybridization (CGH). The analysis indicated that the pN0 tumors carried preferentially overrepresentations of chromosomes 5p, 6p, and 7p and that the pN+ tumors were frequently characterized by deletions on chromosomes 7q, 10q, 11p, 11q, 15q, and 20p and overrepresentations of the chromosomes 19q and 20q. In particular, the use of difference histograms and statistical analysis indicated that the deletions on chromosomes 10q25-q26 and 11p13-p14 were highly significant for metastasizing carcinomas. The findings on chromosome 10q were supported by loss of heterozygosity analysis in the primary tumors and eight synchronous lymph node metastases using four microsatellite polymorphisms. The data suggest that distinct patterns of genetic lesions are responsible for the metastatic phenotype of head and neck squamous cell carcinomas.