Background <p>Choline metabolism, which participates in various biological processes, has been implicated in the development of atherosclerosis and neurological disorders. However, it remains uncertain whether disruptions in the choline metabolism contribute to longitudinal changes in neurological function.</p> Objectives <p>We aimed to prospectively investigate the associations between circulating levels of choline and betaine and neurological function trajectory among patients with ischemic stroke.</p> Methods <p>Data came from the China Antihypertensive Trial in Acute Ischemic Stroke (CATIS). Baseline plasma levels of choline and betaine were measured in 933 participants by ultra-high-performance LC-MS/MS. Group-based trajectory model was employed to identify distinct neurological function trajectories, as measured by NIHSS at admission, 14 days or discharge, and at 3-, 12-, and 24-month follow-up.</p> Results <p>A total of 933 stroke patients were included. Higher choline and betaine levels were generally associated with lower odds of more severe neurological deficit trajectories. Compared with the lowest tertile, the highest choline tertile had adjusted odds ratios (aORs) of 0.68 (95% confidence interval [CI]: 0.44–1.04) for moderate neurological deficits and 0.24 (95% CI: 0.09–0.66) for persistent-severe deficits. Corresponding aORs for betaine were 0.57 (95% CI: 0.37–0.90) and 0.20 (95% CI: 0.08–0.51), respectively. Furthermore, in fully adjusted models, each 1-SD higher log-choline and -betaine was associated with 26% and 28% lower odds of moderate-to-severe neurological deficit. In addition, both choline and betaine improved risk discrimination and reclassification for moderate-to-severe neurological deficit beyond conventional risk factors.</p> Conclusions <p>Our study found that lower plasma levels of choline and betaine were generally associated with moderate and persistent-severe neurological function trajectories.</p> Trial registration <p>NCT01840072; registration date: 2013-04-13.</p>