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We analysed cell-free DNA (cfDNA) in the plasma of patients with both malignant and benign breast lesions by real-time quantitative PCR to determine whether the finding may have diagnostic and prognostic implications. Plasma samples were obtained from 33 patients with breast cancer, 32 patients with benign breast lesions and 50 healthy women as normal controls. Circulatory cfDNA was extracted from the plasma samples and quantified by real-time quantitative PCR for the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene. The mean concentrations of cfDNA in the plasma samples from patients with breast cancer, patients with benign breast lesions and normal controls were 2,285, 1,368 and 1,489 genome equivalents (GE) per millilitre, respectively. The level of cfDNA in the breast cancer group was significantly higher than those in the benign lesion group and control group ( P = 0.007 and 0.013, respectively). These findings were associated with malignant tumour size. The levels of the cfDNA were high in patients with lymph node involvement and distant metastasis. Our results suggest that levels of cfDNA in the plasma are elevated in malignant breast cancer and correlated with tumour size. These findings could have diagnostic and prognostic value for malignant breast tumours. [ABSTRACT FROM AUTHOR]