This study aimed to investigate the correlations of Estrogen Receptor (ER), Progesterone Receptor (PR), human epidermal growth factor receptor 2 (Her-2) and cytokeratin 5/6 (CK5/6) protein expression with histological characteristics features and prognosis of breast Ductal Carcinoma in situ (DCIS). Fortyeight cases of breast DCIS specimen were enrolled in this study. The samples were histologically typed and graded. The immunohistochemical analysis was performed to determine the expression of ER, PR, Her-2 and CK5/6 protein. Results showed that, the positive rates of ER and PR protein expression in non-comedo type DCIS group were significantly higher than those in comedo type DCIS group, respectively (P<0.05), and the positive rate of Her-2 protein expression in non-comedo type group was significantly lower than that in comedo type group (P<0.05). There was no significant difference of CK5/6 protein expression between two groups (P>0.05). There was significant difference of positive rate of ER, PR, Her-2 protein expression among histological grades I-III (P<0.01), with no significant difference of CK5/6 protein expression among three groups (P>0.05). The expression of ER protein was positively correlated with PR protein expression (r=0.764, P<0.001) and negatively correlated with Her-2 protein expression (r=-0.643, P<0.001); the expression of PR protein was negatively correlated with Her-2 protein expression (r=-0.622, P<0.001). In 4 recurrent DCIS cases, Her-2 protein expression was positive in 3 cases. ER, PR and CK5/6 protein expressions were negative in all 4 cases. In conclusion, ER, PR, Her-2 protein expressions are significantly correlated with the histological types and histological grades of breast DCIS. The positive Her-2 protein expression is related to the prognosis of breast DCIS.