<p>The pineal gland is an organ that undergoes significant degeneration with age, and these degenerative changes lead to numerous physiological alterations. This study investigated age-related molecular changes and Alzheimer’s disease (AD)-associated pathology in the human pineal gland using histopathological analyses. This study collected a total of 54 human pineal gland specimens. Of these, 47 were categorised into five age groups: 0–20, 21–40, 41–60, 61–80, and 81–100 years. A further 7 cases with confirmed AD-related neuropathological changes were assigned to the AD group, while matched to 7 controls. Our findings revealed that pineal calcification was initiated as early as age 3, with progressive accumulation of calcification and accompanying cellular loss during the ageing process. A remarkable degree of sexual dimorphism was observed: female-predominant patterns included lipofuscin deposition and pineal cysts, whereas male-predominant characteristics included glial fibrillary acidic protein (GFAP) immunoreactivity and connective tissue expression. Significantly, phosphorylated Tau (P-Tau) and amyloid-beta (Aβ) have recently been detected within the pineal gland. Aβ deposition was positively correlated with age and was markedly elevated in individuals with AD. Furthermore, individuals with AD exhibited marked pineal cellular depletion compared with controls, alongside elevated GFAP expression. Cerebro-spinal fluid analysis further revealed significantly reduced melatonin levels in the AD cohort. Overall, this study systematically elucidated the multidimensional pathological features of the pineal gland during ageing and AD progression, and these findings may open new avenues for mechanistic exploration and precision medicine in AD.</p>