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Several studies indicated the ameliorating effects of flaxseed supplementation on apolipoproteins, although others have conflicting results. Therefore, the present research was conducted in order to accurately and definitively understand the effect of flaxseed on apolipoproteins in adults. All articles published up to Juan 2024 were systematically searched through PubMed, Scopus, Embase, and Web of Science to collect all randomized clinical trials (RCTs). A random effects model was used to measure the combined effect sizes. Also, standardized mean difference (SMD) and 95 % confidence interval (CI) were used to report the combined effect size. Our results showed that flaxseed supplementation significantly reduced apo-BI (SMD: −0.57; 95 % CI: −0.95, −0.19, p = 0.003; I 2 = 83.2 %, heterogeneity p < 0.001) and lipo(a) decreased (SMD: −0.34; 95 % CI: −0.59, −0.09, p=0.007; I 2=30.3 %, heterogeneity p=0.197). However, flaxseed did not change apo-AI levels (SMD: −0.37; 95 % CI: −0.87, 0.13, p = 0.146; I 2 = 89.2 %, p-heterogeneity < 0.001). This meta-analysis has shown that flaxseed supplementation may have beneficial effects on apolipoproteins. Future high-quality, long-term clinical trials are needed to confirm our results. • 18 studies were included in meta-analysis. • Flaxseed supplementation was reduced the levels of apo-BI, and Lipo (a) but not apo-AI. • Flaxseed supplementation may have beneficial effects on apolipoproteins. [ABSTRACT FROM AUTHOR]