Dyslipidemia may influence enzymes and transfer proteins needed to the lipoprotein particle remodeling. Calculated indices and evaluation of lipoprotein particle size have widely been used to predict cardiovascular risk. The aim of this study was to evaluate HDL particle size and LDL particle size estimate based on TG/HDL-C as well as apoB/apoA-I ratio as possible marker and atherogenic indices, respectively, of cardiovascular disease risk in the presence of dyslipidemia. We evaluated 100 individuals of both gender, without treatment with lipid-lowering drugs, 27 normolipidemic and 73 dyslipidemic, such as isolated hypercholesterolemia (n = 16), isolated hypertriglyceridemia (n = 17), low HDL-C (n = 26) and mixed dyslipidemia (n = 14). The HDL particle size did not differ between groups. The TG/HDL-C ratio was higher in groups with isolated hypertriglyceridemia (4.2 ± 1.5), low HDL-C (5.2 ± 3.1) and mixed dyslipidemia (5.3 ± 1.6). The apoB/apoA-I ratio was increased in all groups of dyslipidemia (apoB/apoA-I > 0.5) when compared to normolipidemic (apoB/apoA-I = 0.5, p < 0.001). There was a positive linear correlation between the TG/HDL-C ratio and the apoB/apoA-I ratio in low HDL-C group (r = 0.507, p = 0.008, Spearman). The results suggest that the evaluations of lipoproteins particles remodeling markers and the use of calculated indices may contribute to the evaluation of cardiovascular disease risk when dyslipidemia take place.