Determining acute ischemic stroke (AIS) etiology is crucial for guidance of secondary prevention. Here, the inventors performed a correlation analysis between AIS etiology and AIS thrombus cellular composition and content, as assessed using quantitative biochemical assays. In particular, homogenates of 250 AIS patient thrombi were prepared by mechanical grinding. Platelet, red blood cell, and leukocyte content of AIS thrombi were estimated by quantification of glycoprotein (GP)VI, heme, and DNA in thrombus homogenates. AIS etiology was defined as cardioembolic, non-cardioembolic, or embolic stroke of undetermined source (ESUS), according to the TOAST classification. Cardioembolic thrombi were richer in DNA (35.8 vs 13.8 ng/mg, p<0.001) and poorer in GPVI (0.104 vs 0.117 ng/mg, p=0.045) than non-cardioembolic ones. The area under the receiver operating characteristic curve of DNA content to discriminate cardioembolic thrombi from non-cardioembolic was 0.72 (95% CI, 0.63 to 0.81). With a threshold of 44.7 ng DNA/mg thrombus, 47% of thrombi from undetermined etiology would be classified as cardioembolic with a specificity of 90%. In conclusion, thrombus DNA content may provide an accurate biomarker for identification of cardioembolic thrombi in AIS patients with ESUS.