Low-density-lipoprotein cholesterol (LDL-c) guides lipid-lowering therapy, although other lipid parameters could better reflect cardiovascular disease (CVD) risk. Discordance between these parameters and LDL-c has not been evaluated in metabolic syndrome (MetS) patients. We characterized a comprehensive lipid profile in 177 MetS patients. The 2016 ESC/EAS Guidelines for the Management of Dyslipidemias were used to define LDL-c targets. The atherogenic lipoprotein profile was compared in patients with LDL-c within and above the target. Only 34.4% (61) of patients had mean LDL-c levels within the guidelines and patients with LDL-c above target presented significantly elevated levels of Apolipoprotein B (ApoB), non-high-density lipoprotein cholesterol (non-HDL-c) and oxidized LDL-c. In patients with LDL-c within target, 25%, 31% and 49% presented levels above the recommended range for ApoB, non-HDL-c and oxidized LDL-c, respectively. Patients presented a strong association of LDL-c and non-HDL-c (r = 0.796), ApoB (r = 0.749) and oxidized LDL-c (r = 0.452). Similarly, non-HDL-c was strongly correlated with ApoB (r = 0.857) and oxidized-LDL-c (r = 0.555). The logistic regression model evidenced higher triglycerides and HDL-c and lower ApoB as predictors of having LDL-c within target. Reliance solely on LDL-c could result in missed opportunities for CVD risk reduction. ApoB, oxidized LDL-c, and particularly non-HDL-c, could be valuable parameters to estimate the CVD risk of MetS patients and have the potential to be targeted therapeutically.