Objective To investigate the morphological changes, apoptosis and brainderived neurotrophic factor mRNA（BDNF mRNA）expression in rat conus medullaris induced by cauda equine compression, and to discuss the possible mechanisms. Methods Ninety male SD rats were divided into 3 groups: normal control, sham operation，and cauda equine compressed. The animals were sacrificed and took samples in 30 min, 2 hours,4 hours,8 hours,1 day,3 days,1 week,2 weeks,3 weeks after cauda equine compression model were created. The morphological study concerned with cauda equina and conus medullaris was done under light microscope and transmission electron microscope. TUNEL staining and EM>in situ/EM> hybridization staining were used to investigate apoptosis and BDNF mRNA expression changes. The positive cells in 1mmSUP>2/SUP> were calculated,and the data were disposed through one way analysis of variance. Results Histological observation showed notable alteration of cauda equina and neurons in conus medullaris. The positive cells of TUNEL and BDNF mRNA EM>in situ/EM> hybridization staining increased in 8 hours and 4 hours after cauda equina compressed，and both reached the climax in 3days after cauda equina compressed. At the time 3weeks after cauda equine compressed, the positive cells were still much higher than that of the control groups. Conclusion The compression of cauda equina will result in neurons morphological changes and apoptosis in medullary cone,and cause central neuron unreversible injury. It might be one of the reasons why the prognosis is poor in cauda equina syndrome. Neurons and glial cells may prod