In this study on patients with stroke and IE, we found that: (i) histopathological stains successfully detected microorganisms within cerebral thrombi from IE; (ii) bacterial PCR of cerebral thrombi may provide valuable supplementary diagnostic information in selected cases; (iii) cerebral thrombi from IE patients exhibited distinctive features, including lower red blood cell, increased vWF content, a higher prevalence of NETs with a cell-dominant pattern, and hallmarks of more advanced age. Here, VWF is linked to stroke disorder.