Multiple and extensive alterations in chromosome 9 were detected in thirty-four esophageal squamous cell carcinoma patients, using seventeen polymorphic markers localized to chromosome 9 to detect the loss of heterozygosity (LOH) by polymerase chain reaction techniques. The LOH rates detected in this study range from 42.9 to 80.0%. Three commonly deleted regions mapping to 9p23-p22, 9q13-q22.3, and 9q34 were observed. D9S1812 LOH at 9q22.1 was significantly associated with well- and moderately-differentiated tumors; LOH at D9S768, mapping to 9q13-21.3, indicated that drinking habits are not a significant risk factor for Chinese esophagus cancer. Interestingly, no case of microsatellite instability was observed.