The main purpose of this report is to demonstrate the presence of subfractions in serum HDL and to explore their role in the pathogenesis of thrombotic stroke Preparative untracentrifugation was used to isolate the differing density fractions of serum lipoproteins, and 2-27% polyacrylamide gradient gel electrophoresis was used to identify the character of the HDL subfractions. The study was performed on 59 Chinese males, in whom 31 were patients with thrombotic stroke affecting the cerebral cortex diagnosed by neurological examination and computed tomography; and the others grouped as healthy control. The age and Broca index of both groups were similar. The serum levels of total cholesterol and LDL-cholesterol were normal. However, in the thrombotic stroke group HDL-cholesterol was significantly lower and correlated inversely with both significantly higher levels of VLDL-cholesterol (r=-0.5392, p less than 0.01) and VLDL-triglyceride (r=-0.5866, p less than 0.01). The serum levels of total triglycerides and LDL-triglyceride were also significantly higher in patient with thrombotic stroke. The mean area percentage of HDL2b subfraction measured in the diameter range as determined by gradient gel electrophoresis was significantly lower and HDL2 also showed the same tendency in patients with thrombotic stroke. Our finding was consistent with the postulation that HDL2 or HDL2b in in particular, probably played a more protective role than any other HDL subfractions against thrombotic stroke, one of the major atherosclerotic complications.