High-density lipoprotein (HDL) proteomic study has identified substantial changes associated with various disease states. In the current study, the HDL proteomes in patients with cerebral lacunar infarction (LACI) and control subjects were investigated. A total of 12 LACI patients without evident large vessel occlusions and 12 controls were enrolled in the study. The HDL fraction from each sample was isolated from the plasma by ultracentrifugation. The protemics of the HDL were investigated using nano liquid chromatography coupled to tandem mass spectrometry. There were 55 proteins identified as differentially expressed in the LACI and control groups. Among the 55 proteins, 33 were upregulated and 22 were downregulated in the patients with LACI. The identified proteins were associated with numerous molecular functions, including lipid and cholesterol transport, lipid metabolism, inflammatory response, the complement and coagulation pathway, metal ion metabolism, hemostasis and endopeptidase inhibitory activity. Serum amyloid A, apolipoprotein C (apoC-III) and apolipoprotein A-II (apoA-II) were selected to confirm the proteomics results via western blotting. HDL from the LACI patients exhibited an impaired ability to inhibit the binding of THP-1 cells to endothelial cells compared with the controls (P<0.01). ApoC-III-rich HDL also had a significantly reduced ability to inhibit the binding of THP-1 cells to endothelial cells (P<0.01). The expression of vascular cell adhesion molecule-1 protein by the endothelial cells exhibited a similar pattern of response to the different HDL samples. In conclusion, the present study demonstrates major modifications of the HDL proteome in patients with LACI. The ApoC-III enrichment of the HDL of patients with LACI may cause a reduction in the anti-inflammatory ability of HDL, which may contribute to the progression of the disease.