Breast cancer remains the second most frequent type of cancer in the world and the first among women, and systemic chemotherapy is an adjuvant therapeutic modality that improves survival in a great part of patients. Women with breast cancer, however, frequently show a higher risk of thromboembolism, an event associated to hyperhomocysteinemia and the presence of circulating tumor cells (CTC). Our aim is to correlate the presence of CTCs, detected by the analysis of CK19 and c-erbB2 gene expressions, and the homocysteine plasma levels in the peripheral blood in patients with breast cancer undergoing chemotherapy. Epithelial marker expression (CK19 and c-erbB2) and homocysteine levels were analyzed in a mononuclear fraction of the peripheral blood and plasma, respectively, obtained from 35 patients diagnosed with breast cancer at diagnosis and throughout chemotherapy treatment. No significant relation between the CK19 and c-erbB2 expressions and hyperhomocysteinemia was observed at any moment of the evaluation throughout the chemotherapy treatment (3 and 6 months after the onset). Among clinical data, only menopausal status showed a statistically significant correlation with homocysteine concentration. Although differences in the expressions of the analyzed epithelial markers were detected at 3 and 6 months of chemotherapy treatment, no relation between plasma homocysteine variations and the CK19 and c-erbB2 gene expressions was found in patients under chemotherapy treatment at any moment of the evaluation, suggesting that chemotherapy affects the expressions of the studied genes independently.