To assess the prognostic value of matrix Gla protein (MGP) expression in cases of breast cancer, 9 samples from patients diagnosed with breast cancer who were followed up for more than 10 years were microdissected and then analyzed using Affymetrix U133 Plus 2.0 Arrays. Genes that exhibited significant differences in expression between patients with a good prognosis and those with a poor prognosis were identified. The MGP gene was among the genes up-regulated in cases where the prognosis was poor, indicating that the mRNA levels of MGP are a potential prognostic indicator of breast cancer. However, immunohistostaining of breast tissue microarrays (n=207) did not reveal a correlation between the protein expression of MGP and overall survival, neither was there a correlation between the protein expression of MGP and ER status or bone metastasis. In breast cancer cases, the mRNA level of MGP may be a marker indicating poor prognosis; however, protein expression determined by immunohistostaining is not.