BACKGROUND: Epidemiological studies evaluating the association of vitamin B6, vitamin B12 and methionine with breast cancer risk have produced inconsistent results. METHODS: Pertinent studies were identified by a search in PubMed and Web of Knowledge. Random-effect model was used. Dose-response relationship was assessed by restricted cubic spline. RESULTS: The combined relative risk (95% confidence interval) of breast cancer for the highest vs lowest category of serum pyridoxal 5'-phosphate (PLP, active form of vitamin B6) levels and dietary methionine intake was 0.80 (0.66-0.98, P=0.03) and 0.94 (0.89-0.99, P=0.03), respectively, and the associations of breast cancer with higher serum PLP levels and dietary methionine intake were significant among post-menopausal women, but not among pre-menopausal women. The inverse association between breast cancer risk and dietary vitamin B6 intake, serum vitamin B12 levels and dietary vitamin B12 intake was not significant overall. Linear dose-response relationship was found, and the risk of breast cancer decreased by 23% (P<0.00) for every 100 pmol ml(-1) increment in PLP levels and 4% (P=0.05) for every 1 g per day increment in dietary methionine intake, respectively. CONCLUSION: Serum PLP levels and methionine intake might be inversely associated with breast cancer risk, especially among postmenopausal women, which need to be confirmed.