<p>Branched-chain amino acids (BCAAs) have been associated with cognitive function, with conflicting evidence suggesting both potential benefits and risks in neurodegenerative diseases such as Alzheimer’s disease (AD) and mild cognitive impairment (MCI), highlighting the need for further investigation. This study aimed to explore the relationship between total BCAAs, cognitive function, and brain structure, specifically examining hippocampal volumes and their potential mediating effects in individuals with AD, MCI, and cognitively normal (CN) individuals. Cognitive function was assessed using the CDR-SB scale, total BCAAs were measured in serum through NMR metabolomics, and hippocampal volumes were evaluated using voxel-based morphometry (VBM). This study found that elevated total BCAAs were initially associated with increased hippocampal volumes in MCI, though this relationship became non-significant after adjusting for confounding factors such as age, gender, education, and ApoE ɛ4 status. Increased hippocampal volumes, however, remained consistently linked to better cognitive function in both MCI and AD, regardless of adjustments. Importantly, mediation analysis revealed indirect effects of elevated total BCAAs on improved cognitive function via increased hippocampal volumes, with being significant only in MCI before controlling for confounders; however, this mediation relationship disappeared after adjusting for age, gender, education, and ApoE ɛ4 status. These findings suggested that BCAAs may be associated indirectly with improved cognitive function, with increased hippocampal volume acting as a key mediator, particularly in MCI. However, the effects of BCAAs were sensitive to confounding factors such as age, gender, education, and APOE-ɛ4 status, which we accounted for in our analyses; however, other unmeasured factors such as dietary intake may also affect the observed associations, underscoring the importance of considering these variables in future studies.</p>