Background: Anaphylaxis is the most severe manifestation of allergic disorders. Diagnostic and understanding of molecular mechanisms need to improve. Extracellular vesicles (EVs) play a key role in cellular communication offering new possibilities to unravel patient-based particularities. The aim of this study is to analyze the protein profile of anaphylaxis-derived EVs providing a resource of potential markers for anaphylactic reactions, and to characterize their molecular mechanisms. Methods: EVs were isolated from 86 plasma samples (collected from 43 patients) during the acute phase of anaphylaxis (AnEVs) and at their baseline (BEVs). For comparison, EVs were characterized and their protein patterns were analyzed by mass spectrometry-based quantitative proteomics (LC-MS/MS). System Biology Analysis (SBA) was applied to identify main canonical pathways and molecules involved. In addition, in vitro permeability assays based on EVs-endothelial cells (ECs) were performed. Results: Differential proteomic analysis performed in 10 EVs paired patients’ samples identified 1206 proteins of which 99 were modulated in the AnEVs signature. CDC42, Ficolin-2 and S100A9 enrichment was confirmed in a larger cohort of patients. SBA revealed diverse group of immune proteins as the main canonical pathways altered in AnEVs. Thus, leukocyte extravasation and granulocyte adhesion-diapedesis processes stand out. In addition, marked-EVs from anaphylactic patients were captured by ECs decreasing the resistance of human endothelial monolayers. Conclusion: Our findings identify for the first time a differential EVs pattern signature in anaphylaxis revealing a source of potential biomarkers. Furthermore, these vesicles could participate in altered immune molecular mechanisms and present a role increasing vascular permeability.