Background and aims: The association between amino acids and small dense low-density lipoprotein cholesterol (sdLDL-C) and remnant-like particle cholesterol (RLP-C) remains poorly understood. This study aims to investigate the association between plasma essential amino acids (EAAs) and atherogenic lipid profiles. Methods: Plasma amino acid levels of 475 individuals were measured using liquid chromatography-mass spectrometry. SdLDL-C, RLP-C, and other lipid components were evaluated. Associations between EAAs and lipid components or dyslipidemia were determined using correlation analysis and multivariate logistic regression. Results: Concentrations of plasma branched-chain amino acid (BCAA) were positively correlated with sdLDL-C, RLP-C, and triglycerides (TG) levels, but inversely correlated with high-density lipoprotein cholesterol (HDL-C). In contrast, threonine concentration was inversely correlated with sdLDL-C, RLP-C, and TG. Compared with the lowest tertile, individuals in the highest tertile of plasma total BCAAs level had an odds ratio (OR) of 2.33 (95% confidence interval [CI]: 1.35, 4.03) for the risk of high sdLDL-C, 3.63 (95% CI: 1.69, 7.80) for the risk of high RLP-C, 3.10 (95% CI: 1.66, 5.80) for the risk of high TG, and 3.67 (95% CI: 2.00, 6.73) for atherogenic lipid triad (all p < 0.01). In contrast, compared with the lowest tertile, individuals in the highest plasma threonine tertile had a 43% lower OR for high sdLDL-C, 56% lower OR for high TG, and 55% lower OR for lipid triad risk (all p < 0.05). Conclusions: Among the EAAs evaluated, elevated plasma BCAAs were significantly associated with increased risk of atherogenic lipid profile. In contrast, elevated threonine was associated with reduced risk of atherogenic lipid profile.