Abstract: [Abstract] Objective To investigate the relations between the gene expression of PR, HER-2 and Ki-67 in invasive ductal breast cancer with ER negative and clinical pathological indexes. Methods One thousand three hundred thirty nine cases with invasive breast cancer were selected. Among them, there were 403 cases with ER negative. PR, HER-2 and Ki-67 expression were analysed by the Spearman rank correlation. At the same time, relations between PR, HER-2 and Ki-67 expression and clinic indexes were retrospectively analysed. Results The positive rates of PR, HER-2 and Ki-67 were 8.9%（36/403）、26.8%（108/403）and 98.3%（396/403）, respectively. The expression of PR had statistical differences between age, tumor sizes and the expression of P53 (P <0.05), and had not statistical differences in histologic grade and lymph node metastasis (P >0.05). However, the expression of HER-2 was significantly statistical differences in clinic indexes (P <0.05). Moreover, the expressions between PR, HER-2 and Ki-67 were also correlated. Finally, the expressions between Ki-67 and HER-2 were significantly correlative(r =0.941，P =0.000). Conclusion The expressions of HER-2 are related with clinical pathological features in breast cancer with ER negative. The expression of Ki-67 can be regarded as an important index for the expression condition of HER-2.