The aim of this study was to classify bilateral breast cancers (BBCs) into two groups according to histopathological or molecular subtypes of the two breast diseases in each patient and to study their characteristics in relation to survival outcomes. Fifty-six BBC patients were enrolled in the study. They were classified according to whether the two breast diseases were of the same or different histopathological subtypes (defined as S-his or D-his groups) and molecular subtypes (defined as S-mole and D-mole groups). Progression-free survival (PFS), overall survival (OS), and important characteristics were then compared between the groups. We observed that the PFS and OS of the S-mole and D-mole groups failed to reach a significant difference. However, D-his BBC patients enjoyed longer PFS than their S-his counterparts, although the OS was similar. To explore the reason for the extended PFS in D-his BBC patients, we first focused on the possible prognostic contribution by various histopathological subtypes in the groups. We compared the proportion of infiltrating ductal carcinoma, infiltrating lobular carcinoma, and other breast cancer subtypes in the D-his and S-his groups, and demonstrated that they were not associated with longer PFS. We then examined age, menopausal status, tumor, node, and metastasis (TNM) stage, expressions of estrogen receptor (ER), progesterone receptor (PR) and Ki67, and metastasis to lymph nodes, viscera, and bone. The results indicated no significant between-group differences in age, TNM stage, ER/PR expression, and metastasis to viscera and bone. However, significantly lower levels of Ki67and decreased lymph node metastasis rate were associated with D-his BBC patients, which might explain the observed longer PFS. In comparison to S-his, D-his BBC patients had longer PFS, which was associated with lower levels of Ki67 and a decreased lymph node metastasis rate.