BackgroundMetabolomics is increasingly being utilized in IS research to elucidate the intricate metabolic alterations that occur during ischemic stroke (IS). However, establishing causality in these associations remains unclear between metabolites and IS subtypes. In this study, we employ Mendelian randomization (MR) to identify specific metabolites and investigate potential causal relationships between metabolites and IS subtypes.MethodsMR analysis was conducted using genome-wide association study (GWAS) summary data. We obtained 1,091 blood metabolites and 309 metabolite ratios from the GWAS Catalog (GCST90199621-90201020), which gene sequencing data from 8,299 individuals from the Canadian Longitudinal Study. We obtained GWAS summary statistics for IS subtypes which include large artery stroke (LAS), cardioembolic stroke (CES), and small vessel stroke (SVS) from the MEGASTROKE consortium that included 446,696 cases of European ancestry and 406,111 controls of European ancestry. The primary analysis utilized inverse-variance weighted (IVW) method. To validate our results, we performed supplementary analyses employing the MR-Egger, weighted median, simple mode, and weighted mode methods. Heterogeneity and pleiotropy were assessed through Cochran’s Q test, MR-Egger intercept test, and leave-one-out analysis.ResultsThe study assessed the possible causality of serum metabolites in the risk of IS subtypes. The discovery of significant causal links between 33 metabolites and 3 distinct IS subtypes.ConclusionMetabolites show significant potential as circulating metabolic biomarkers and offer promise for clinical applications in the prevention and screening of IS subtypes. These discoveries notably advance our comprehension of the molecular processes specific to IS subtypes and create avenues for investigating targeted treatment approaches in the future.