Objective To explore the effect of caspase-9 inhibitor on low fetal bovine serum (FBS)-induced apoptosis in cartilage endplate chondrocytes in SD rat vertebrae. Methods Disc cartilage endplates were obtained from 3-month old SD rats and subjected to sequential digestion to harvest chondrocytes for primary culture, and apoptosis was induced by 1% FBS for 48 hours. Three groups of chondrocytes were treated by 1% FBS, caspase-9 inhibitor (Z-LEHD-FMK) and DMSO, respectively. After 48 hours, apoptosis was detected by DAPI staining and flow cytometry. The expression of procaspase-9, active caspase-9 and active caspase-3 was monitored by Western blot. Results Compared with the 1% FBS group (40.8±0.84)% and DMSO group (40.2±1.56)%, the apoptosis rate of the caspase-9 inhibitor group (26.3±2.56)% was significantly lower (P<0.05). The expressions of active caspase-9 and active caspase-3 in the caspase-9 inhibitor group were significantly lower than those in the other two groups (P<0.05). Conclusions Caspase-9 inhibitor can inhibit low FBS-induced apoptosis in cartilage endplate chondrocytes of rat vertebrae, and might become a new drug for the treatment of disc degeneration.