Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1), which regulates the conformation of Pro-directed phosphorylation sites, has been identified as a critical catalyst involved in multiple oncogenic signaling pathways. Recently, it has been demonstrated that several putative functional polymorphisms of PIN1 gene were associated with cancer risk. This study examined whether genetic polymorphisms in promoter of PIN1 are associated with esophageal carcinoma susceptibility. Two common polymorphisms in PIN1, rs2233678 (-842G>C) and rs2233679 (-667C>T) were genotyped in this hospital-based case-control study of 699 esophageal carcinoma patients and 729 healthy controls. The results revealed that compared with the most common -842GG genotype carriers, the carriers of -842C variant genotypes (GC+CC) had significantly decreased risk of esophageal carcinoma [odds ratio (OR) = 0.55, 95 % CI = (0.40-0.75), P = 0.001]. No association was observed between the -667C>T polymorphism and the risk of esophageal carcinoma. Furthermore, we found that the haplotype of 'C(-842)-C(-667)' had a greater protected effect [OR = 0.67, 95 % CI = (0.47-0.96), P = 0.021]. Functional assay revealed that -842C variant genotypes (GC+CC) carriers had a lower transcription activity and mRNA expression level than the -842GG carriers. These results indicated that -842G>C genetic variant in PIN1 promoter may decrease the promoter activity, resulting in changes in the levels of PIN1 and modifying cancer susceptibility.