Objective To investigate the relationship between caspase-9 (-Ex5+32 G/A) gene polymorphisms, Schneiderman score of magnetic resonance imaging (MRI) in lumbar disc degeneration and the expression of caspase-9 in degenerative nucleus pulposus. Methods The peripheral venous blood and prominent nucleus pulposus were obtained from 105 patients with lumbar disc herniation. Genomic DNA was extracted and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The caspase-9(-Ex5+32 G/A) gene polymorphisms were analyzed in all DNA samples. The expression of caspase-9 in the tissues was detected by immunohistochemical SP staining. The t test was used to analyze the difference between the genotypes and the expression of caspase-9 in intervertebral disc nucleus. Pearson correlation analysis was performed to assess the association between caspase-9 expression in nucleus pulposus and the MRI score of lumbar disc. Results MRI analysis showed that the patients with AA genotype had the highest MRI scores, but there were no significant differences in MRI scores among patients with AA, GA, and GG genotypes. Compared with GG genotype carriers, AA genotype carriers had a statistically significant difference in the expression of caspase-9 in nucleus pulposus. There was no correlation between the MRI score of lumbar disc degeneration and the expression of caspase-9 in the degenerated nucleus pulposus. Conclusion The caspase-9(-Ex5+32 G/A) gene polymorphism is associated with the expression of caspase-9 in the degenerative nucleus pulposus. However, the MRI Schneiderman score is not significantly correlated with the expression of caspase-9 in degenerative nucleus pulposus.