Cystathionine β-synthase (CBS)-deficient patients are prone to vascular thrombosis. In contrast, Cbs −/− mice show no abnormalities in blood coagulation. To identify molecular basis underlying these disparately different thrombotic phenotypes, we analyzed plasma proteomes of Cbs −/− vs. Cbs +/+ mice (8-month-old, 12/group, sex-matched) and CBS −/− vs. CBS +/+ humans (37 ± 7-year-old, 10-14/ group, sex-matched) using label-free mass spectrometry. We identified 117 and 41 differentiating plasma proteins in Cbs −/− mice and CBS −/− humans, respectively. Twenty-one proteins were shared between CBS −/− humans and Cbs −/− mice, with sixteen changed in the opposite direction. Proteins involved in blood coagulation and complement/coagulation cascades represented a greater fraction of the differentiating proteins in CBS −/− patients (51%) than in Cbs −/− mice (21%). Top canonical pathways, identified by Ingenuity Pathways Analysis, such as LXR/RXR, FXR/RXR activation (− log[P-value] = 30-31) and atherosclerosis signaling (− log[P-value] = 10-11) were similarly affected in Cbs −/− mice and CBS −/− humans. The Coagulation System was affected stronger in CBS −/− humans than in Cbs −/− mice (− log[P-value] = 15 vs. 10, respectively) while acute phase response and complement system were affected stronger in Cbs −/− mice (− log[P-value] = 33 and 22, respectively) than in humans (− log[P-value] = 22 and 6, respectively). Other pathways, including IL-7 signaling and B cell development were affected only in Cbs −/− mice. Taken together, our findings suggest that differences in these processes, in particular in the Coagulation System, could account for the thrombotic phenotype in CBS −/− patients and the absence of thrombosis in Cbs −/− mice. Overall, our findings suggest that Cbs −/− mice have a better adaptive response to protect from prothrombotic effects of hyperhomocysteinemia than CBS −/− humans. Patients with cystathionine β-synthase (CBS) deficiency, a rare inborn error of metabolism caused by mutations in the CBS gene, have severely elevated levels of the sulfur-amino acid homocysteine (Hcy) 1 and its metabolites 2. The only known source of Hcy in the human body is the dietary protein methionine, which is converted to Hcy in a sequence of three consecutive reactions with AdoMet and AdoHcy as intermediates. Hcy is further metabolized via three pathways, affording cysteine, methionine, or Hcy-thiolactone 3. The metabolic conversion of Hcy to cysteine is impaired in CBS-deficient patients, causing severe hyperhomocysteinemia (HHcy) 1 and