Skull base chordoma is a rare tumor with unknown risk factors. Werner syndrome, which is caused by a mutation in the WRN gene, is a disease of progeria, resembling the pathological process of aging. The present study aimed to provide data on the possible association between skull base chordoma and the single- nucleotide polymorphism (SNP) rs1346044 of the WRN gene. Between July, 2010 and September, 2012, a total of 65 patients with pathologically confirmed skull base chordoma and 65 control subjects were enrolled in this case-control study. The clinical data of the skull base chordoma patients were documented and the rs1346044 site in all the enrolled subjects was analyzed by sequencing and statistically compared using SPSS software. The A allele was the dominant allele of the rs1346044. The comparisons of genotype distributions and allele frequencies did not reveal any significant difference between the groups [P=0.383, 95% confidence interval (CI): 0.346-1.505]. The clinicopathological factors were assessed and no statistically significant difference was observed. In conclusion, the present study suggested that there is no association between rs1346044 SNP and skull base chordomas, at least in the population analyzed.