Several environmental factors have been implicated in the etiology of esophageal cancer (EC). The purpose of this study was to assess the likelihood that variation in the SLC11A1 gene contributes to EC susceptibility, possibly due to its role in inflammation and iron metabolism. The regions of the gene containing potential functional polymorphisms, including the promoter region and exon 2, were investigated. The study cohort included 105 EC South African Colored patients with squamous cell carcinoma (SCC) and 110 population-matched controls, with South African Colored referring to individuals of mixed ancestry. A significantly decreased frequency of the -237C-->T promoter polymorphism was observed in the patient group with EC compared with the population-matched control group (P < 0.002, chi(2) with Yates's correction=7.87). A statistically significant disease association was also observed with allele 3 of the 5'-(GT)n promoter polymorphism (P < 0.0006, chi(2) with Yates's correction=10.16), but only in the absence of the T-allele at nucleotide position -237 following allelic stratification. Four novel variants were identified in intron 1 (IVS1-28C-->T) and exon 2 (112G-->A, 148delGACCAGCCC, 157insGACCAGCCCAG). The novel intronic polymorphism, IVS1-28C-->T, was also significantly associated with EC (P < 0.05, chi(2) with Yates's correction=2.52). We demonstrate association of genetic variation in both the promoter region and intron 1 of the SLC11A1 gene with EC susceptibility.