Abstract Microcephalin 1 (MCPH1) has a crucial role in the DNA damage response by promoting the expression of checkpoint kinase 1 (CHK1) and breast cancer susceptibility gene 1 (BRCA1). MCPH1 containing BRCT domain has been suggested as a tumor suppressor in breast and ovarian cancers. We analyzed the effect of both protein expression and MCPH1 polymorphisms in breast cancer patients. Low nuclear expression of microcephalin was present in 52.4% of breast cancers and was associated with allele T in rs2912010 (p=0.046). However, cytoplasmic microcephalin expression increased with increasing grade (p=0.010). An association between low nucleus microcephalin expression and allele T was identified in rs2912010 (p=0.046). After data analysis, allele distribution of the MCPH1 polymorphisms was not different between breast cancer patients and healthy controls. But the polymorphism was associated with negative status for ER (rs2912010/C2302T; p=0.032, rs1057090/C2358T; p=0.027, rs2912016/C2494A; p=0.024), and allele T in both rs2912010 and rs1057090 was associated with increasing tumor grade (rs2912010; p=0.040, rs1057090; p=0.043) in breast cancer. We are first to report that association of MCPH1 protein expression and its polymorphisms in breast cancer. The MCPH1 polymorphisms and protein expression were associated with tumorigenesis in breast cancer and may be a useful biomarker for identification of the aggressive types of breast cancer.