Arterial thromboembolism (ATE) is a common complication of cats with cardiomyopathy (CM), but little is known about the pathophysiology of ATE. In people, high plasma concentrations of homocysteine and low B vitamin concentrations are risk factors for peripheral vascular disease. In addition, low plasma arginine concentrations have been linked to endothelial dysfunction. The purpose of this study was to compare concentrations of homocysteine, B vitamins, and amino acids in plasma of normal cats to those of cats with CM and ATE. Plasma concentrations of homocysteine, vitamin B6, vitamin B12, folate, and amino acids were measured in 29 healthy cats, 27 cats with CM alone, and 28 cats with both CM and ATE. No differences were found between groups in homocysteine or folate. Mean vitamin B12 concentration (mean ± standard deviation) was lower in cats with ATE (866 ± 367 pg/mL) and cats with CM (939 ± 389 pg/mL) compared with healthy controls (1,650 ± 700 pg/mL; P < .001). Mean vitamin B6 concentration was lower in cats with ATE (3,247 ± 1,215 pmol/mL) and cats with CM (3,200 ± 906 pmol/mL) compared with healthy control animals (4,380 ± 1,302 pmol/mL; P= .005). Plasma arginine concentrations were lower in cats with ATE (75 ± 33 nmol/mL) compared with cats with CM (106 ± 25 nmol/mL) and healthy control animals (96 ± 25 nmol/ mL; P < .001). Vitamin B12 concentration was significantly correlated with left atrial size. We interpret the results of this study to suggest that vitamin B12 and arginine may play a role in CM and ATE of cats.