Although several cytogenetic events of the tumor progression cascade have been identified in the past, the specific types of chromosomal alterations that lead to the development of lymph node metastases are still unknown. Operative specimens of 20 patients (10 patients with metastasizing tumors, 10 patients with nonmetastasizing tumors) with squamous cell carcinomas of the oropharynx and hypopharynx, along with the corresponding lymph node metastases, were investigated by quantitative DNA measurements and comparative genomic hybridization (CGH). Nonmetastasizing tumors (N0) displayed overrepresentations on chromosomes 10q (8 cases); 5p (7 cases); 3q and 20q (6 cases each); 8q (5 cases); 1p and 21q (4 cases each); 7p and 20p (3 cases each); and 2p, 15q, and 19q (2 cases each). Loss of chromosomal material was found on 5q, 9p, and 14q (2 cases each). Metastasizing tumors (N+) demonstrated overrepresentations on chromosomes 5p, 15q, and 22q (6 cases each); 3q and 11q13 (5 cases each); 20p and 21q (4 cases each); and 10q (3 cases). In 2 cases, an overrepresentation of the chromosomal arm 3q was accompanied by a loss of chromosomal arm 3p. Less frequent overrepresentations were observed on chromosomes 1q and 17q. Deletions were found on chromosomes 18q (3 cases), 3p, 4q, 5q, and 19p (2 cases each); and sporadic deletions occurred on 2q, 6q, 8p, 9p, 10p, 13q, 14q, 15q, and 16q. Whereas overrepresentations on chromosomes 1p and 7p occurred exclusively in N0 tumors, overrepresentations on chromosomes 1q, 11q, and 22q, along with deletions on 18q, were only observed in N+ tumors. Quantitative DNA measurements revealed a significantly higher percentage of aneuploid cells and a higher degree of DNA entropy in the N+ tumors. Chromosomal overrepresentations on chromosomes 1q, 8q, 11q, 18q, and 19q occurred more frequently in the metastases than in the corresponding primary tumors. Pairwise analysis of chromosomal alterations in the primary tumors and associated lymph node metastases revealed a genetic relationship, although a greater number of chromosomes on average were affected in the lymph node metastases. Quantitative DNA measurements demonstrated greater aneuploid values in the metastases. Recurring patterns of chromosomal alterations in N0 and N+ tumors were demonstrated in this study. In general, metastasizing tumors are characterized by overrepresentations on chromosomes 11q13 and 22q, and deletions on 18q. These aberrations suggest an elevation along the tumor progression cascade.