Esophageal cancer is the fourth most prevalent malignancy in China. So far, the genetic events involved in esophageal cancer remain largely unknown. To identify chromosomal alterations in this disease, comparative genomic hybridization was performed on 25 primary tumors of esophageal squamous cell carcinomas. Results exhibited nonrandom copy number changes in chromosome DNA, with higher incidence in gain than in loss. The average gains and losses per patient were 7.76 and 4, respectively. The most common gains were 3q (20/25), 1q (15/25), 8q (15/25), 20p (12/25), 20q (11/25), 5p (10/25), 15q (8/25), and 9q (8/25) with two minimal amplification loci mapped to chromosomal regions of 8q24 (2 cases) and 11q13 (7 cases). High-level amplification was observed at 3q (8 cases), 5p (4 cases), and 8q (4 cases). Losses at 3p (10/25), 13q (8/25), 18q (7/25), Xp (7/25), 4 (6/25), 9p (6/25), 14q (6/25), 18p (6/25), and 21q (6/25) were identified. Remarkably, ten cases showed both loss of the entire 3p and overrepresentation of almost the whole 3q. No significant differences in stage or grade of tumor were found for DNA copy number changes. The results provided candidate regions for potential oncogenes and tumor suppressor genes related to Chinese esophageal cancer, to which further molecular studies should be addressed.