Caspase-9 (CASP-9) is an initiator caspase protease for apoptosis, and plays an important role in the development and progression of lumbar disc disease (LDD). The expression and/or activity of CASP-9 are significantly enhanced in the degenerated disc. The polymorphism in the promoter region of CASP-9 enhances the transcriptional activity of this gene, thereby modulating the susceptibility to LDD. The current study investigated the relationship between the CASP-9 -1263A/G (rs4645978) and -712C/T (rs4645981) polymorphisms and discogenic low back pain (LBP). The CASP-9 -1263A/G and -712C/T genotypes in this study were defined by polymerase chain reaction in 154 patients with discogenic LBP and 216 controls that were frequency-matched by age, gender, and occupation. The results showed that the CASP-9 -1263 GG genotype, compared with the AA and AG genotypes [odds ratio (OR) = 1.997, 95% confidence interval (95% CI) = 1.216-3.279, p = 0.006] or the AA genotype (OR = 2.760, 95% CI = 1.464-5.203, p = 0.002), is associated with a significant increased risk of discogenic LBP, but the -712 TT or TT and CT genotypes do not contribute to discogenic LBP compared with the CC genotype (OR = 0.547, 95% CI = 0.200-1.494, p = 0.234 and OR = 0.669, 95% CI = 0.439-1.021, p = 0.062, respectively). These results indicated that the CASP-9 -1263A/G polymorphism is associated with a high risk of discogenic LBP.