Glycosaminoglycans (GAGs) are functionally important molecules of the arterial wall and play a crucial role in atherogenesis. Chondroitin sulfate/dermatan sulfate proteoglycans (CS/DSPGs) participate in several biological events through their GAG chains, and are also involved in the development of atherosclerosis. The aim of this study was to compare the pre- and post-operative levels of CS in serum of patients after coronary artery bypass graft surgery using a highly sensitive reversed-polarity capillary electrophoresis method and to investigate the correlation of CS with common biochemical lipid markers. It was found that CS values were significantly higher for all patients post-operatively and, furthermore, CS levels were statistically correlated to apolipoprotein A and B levels. Notably, the pre-operational lipid profile of the patient may be indicative of the values of 4-sulfated CS post-operationally. Furthermore, the obtained results highlight the clinical significance of CS levels in serum, since they may provide complementary information for the latent inflammatory state of the patient.