Chronic cerebrovascular hypoperfusion is a high-risk factor for Alzheimer’s disease(AD) as it is conducive to beta amyloid(Ab) over-production. Brainderived neurotrophic factor(BDNF) is a member of the neurotrophin family widely expressed in the central nervous system. The structure of the rat BDNF gene is complex, consisting of eight non-coding exons(I–VIII) and one coding exon(IX). The BDNF gene is transcribed from multiple promoters located upstream of different 50 noncoding exons to produce a heterogeneous population of BDNF m RNAs. S-adenosylmethionine(SAM) produced in the methionine cycle is the primary methyl donor and the precursor of glutathione. In this study, a cerebrovascular hypoperfusion rat model and an Ab intrahippocampal injection rat model were used to explore the expression profiles of all BDNF transcripts in the hippocampus with chronic cerebrovascular hypoperfusion or Ab injection as well as with SAM treatment. We found that the BDNF m RNAs and protein were down-regulated in the hippocampus undergoing chronic cerebrovascular hypoperfusion as well as Ab treatment, and BDNF exons IV and VI played key roles. SAM improved the low BDNF expression following these insults mainly through exons IV and VI.These results suggest that SAM plays a neuroprotective role by increasing the expression of endogenous BDNF and could be a potential target for AD therapy. Chronic cerebrovascular hypoperfusion is a high-risk factor for Alzheimer’s disease (AD) as it is conducive to beta amyloid (Ab) over-production. Brain derived neurotrophic factor (BDNF) is a member of the neurotrophin family widely expressed in the central nervous system. The structure of the rat BDNF gene is complex, consisting of eight non-coding exons (I-VIII) and one coding exon (IX). The BDNF gene is transcribed from multiple promoters located upstream of different 50 noncoding exons to produce a heterogeneous population of this BDNF m RNAs. S-adenosylmethionine (SAM) produced in the methionine cycle is the primary methyl donor and the precursor of glutathione. In this study, a cerebrovascular hypoperfusion rat model and an Ab intrahippocampal injection rat model were used to explore the expression profiles of all BDNF transcripts in the hippocampus with chronic cerebrovascular hypoperfusion or Ab injection as well as with SAM treatment. We found that the BDNF m RNAs and protein were down- regulated in the hippocampus undergoing chronic cerebrovascular hypoperfusion as well as Ab treatment, and BDNF exons IV and VI played key roles. SAM improved the low BDNF expression following these insults mainly through exons IV and VI. These results suggest that SAM plays a neuroprotective role by increasing the expression of endogenous BDNF and could be a potential target for AD therapy.