Central role of astrocyte elevated gene-1 (AEG-1) in regulating diverse aspects of hepatocellular carcinoma (HCC) pathogenesis and association of its overexpression with HCC progression has been demonstrated. The positive regulatory regions of AEG-1 promoter contain several putative transcription factor binding sites critical for basal promoter activity. In this study, the aim was to explore the association of AEG-1 promoter variant with HCC. In this study, the human AEG-1 promoter including the region -538 to -42 was explored in 53 HCC patients and 108 healthy controls. The polymerase chain reaction-sequencing method was used for investigating AEG-1 promoter polymorphisms. A novel mutation in AEG-1 promoter in human HCC patients at a potential AP-2 binding site was explored. An A>C mutation was observed in -483 of AEG-1 promoter in 4 out of 53 HCC patients but not in 108 control individuals. Sequencing data showed genetic variations in 11 HCC patients and 3 healthy controls. Among them, one novel SNP was found in activator protein-1 (AP2), a transcription factor binding site (-483 A to C) that may be associated with the susceptibility to HCC (P = 0.012) but no associations were found for other observed variations. This mutation could be tumor-specific. AEG-1 promoter variant -483 A>C may be associated with the susceptibility to HCC in Iranian population. To our knowledge, this is the first study that has reported this association with the susceptibility to HCC. Therefore, further studies need to be conducted in larger sample sizes and other populations to validate these findings.