Esophageal squamous cell carcinoma (ESCC) is one of the most common and deadly cancers in Japan. In this study we performed fluorescent in situ hybridization (FISH) and loss of heterozygosity (LOH) analysis for chromosome 18q in ESCC cells to investigate allelic imbalance of chromosome 18q in ESCC. In the FISH analysis, only one signal for chromosome 18q was detected in TE-1 esophageal cancer cells, whereas two signals were detected in TE-2 cells. Two of five resected ESCC samples from patients showed loss of one copy of chromosome 18q. To construct a precise deletion map of chromosome 18q, LOH analysis was performed using 30 microsatellite markers localized to chromosome 18q. LOH was observed in 31 of 46 ESCC samples (67.4%) for at least one locus on chromosome 18q. LOH frequency for individual markers varied from 18.5% (D18S460) to 48.4% (D18S866). Thirteen of 46 ESCC samples (28.3%) showed the loss of most of the long arm of chromosome 18. Lymph node metastasis and vein invasion were significantly associated with the deletion of chromosome 18q. Loss of chromosome 18q may play an important role in the progression of ESCC.