According to the International Agency for Research on Cancer (IARC) more than 10% of cancers can be explained by inadequate diet and excess body weight. Breast cancer is the most common cancer affecting women. The goal of our study is to clarify the relationship between ω3 fatty acids (FA) carried by different lipoproteins and breast cancer (BC) severity, according to two approaches: through clinic-biological data and through in vitro breast cancer cell models. The clinical study has been performed in sera from a cohort of BC women (n = 140, ICO, France) whose tumors differed by their hormone receptors status (HR− for tumors negative for estrogen receptors and progesterone receptors, HR+ for tumors positive for either estrogen receptors or progesterone receptors) and the level of proliferation markers (Ki-67 ≤ 20% Prolif− and Ki-67 ≥ 30% Prolif+). Lipids and ω3FA have been quantified in whole serum and in apoB-containing lipoproteins (Non-HDL) or free of it (HDL). Differences between Prolif− and Prolif+ were compared by Wilcoxon test in each sub-group HR+ and HR−. Results are expressed as median [25th–75th percentile]. Plasma cholesterol, triglycerides, HDL-cholesterol and Non-HDL cholesterol did not differ between Prolif− and Prolif+ sub-groups of HR− and HR+ patients. Plasma EPA and DHA concentrations did not differ either. In the HR− group, the distribution of EPA and DHA between HDL and Non-HDL differed significantly, as assessed by a higher ratio between the FA concentration in Non-HDL and HDL in Prolif− vs. Prolif+ patients (0.20 [0.15–0.36] vs. 0.04 [0.02–0.08], p = 0.0001 for EPA and 0.08 [0.04–0.10] vs. 0.04 [0.01–0.07], p = 0.04 for DHA). In this HR− group, a significant increase in Non-HDL EPA concentration was also observed in Prolif− vs. Prolif+ (0.18 [0.13–0.40] vs. 0.05 [0.02–0.07], p = 0.001). A relative enrichment on Non-HDL in EPA and DHA was also observed in Prolif− patients vs. Prolif+ patients, as assessed by a higher molar ratio between FA and apoB (0.12 [0.09–0.18] vs. 0.02 [0.01–0.05], p < 0.0001 for EPA and 1.00 [0.73–1.69 vs. 0.52 [0.14–1.08], p = 0.04 for DHA). These data were partly confirmed by an in vitro approach of proliferation of isolated lipoproteins containing EPA and DHA on MDA-MB-231 (HR−) and MCF-7 (HR+) cell models. Indeed, among all the studied fractions, only the correlation between the EPA concentration of Non-HDL was confirmed in vitro, although with borderline statistical significance (p = 0.07), in MDA-MB-231 cells. Non-HDL DHA, in the same cells model was significantly correlated to proliferation (p = 0.04). This preliminary study suggests a protective effect on breast cancer proliferation of EPA and DHA carried by apo B-containing lipoproteins (Non-HDL), limited to HR− tumors.