Lipoprotein aggregation is generated by hydrophobic nature of lipoproteins that is known to be one of the causes of atherosclerosis. Low density lipoproteins (LDL) has been extensively studied in this respect but not chylomicrons. There is strong evidence that post-prandial triacylglycerol-rich lipoproteins are atherogenic. Because biophysical properties of lipoproteins are largely determined by their lipid compositions, hydrophobic nature of thoracic lymph duct chylomicrons obtained from rats given different fats or oils by gavage was investigated by vortexing-induced aggregation and hydrophobic interaction chromatography. Contrary to LDL, vortexing did not cause aggregation in chylomicrons. Vortexing of fish oil and butter chylomicrons resulted in more prominent reduction in absorbances compared with chylomicrons from other sources that might indicate less micelle stability. Hydrophobic interaction chromatography of fish oil, palm oil and olive oil chylomicrons yielded three fractions, whereas that of sunflower, margarine and butter chylomicrons gave rise to two fractions. These results suggest that surface hydrophobicity of chylomicrons might be heterogenous. Our results also demonstrate that fish oil chylomicrons have less hydrophobicity and lower stability against vortexing compared with chylomicrons from other sources. Considering beneficial effects of fish oil in cardiovascular health, less hydrophobicity together with lower stability might provide an additional atherogeneicity index for lipoproteins.