Background: Histologic heterogeneity of tumors is well documented; however, the molecular heterogeneity is not well understood, especially relative to driver mutations within clonal populations and their prognostic and predictive value. Methods: Molecular profiling of breast cancers (BCs) at a single institution were analyzed for differences in clonal populations within the same breast, bilateral synchronous BCs, and/or within primary and paired locally recurrent or metastatic tumors. Gene alterations (GAs) were identified by next generation sequencing (NGS). GAs were compared in 9 synchronous BCs and 48 primary/recurrent paired BCs. Estrogen receptor (ER), progesterone receptor (PR), androgen receptor (AR), were evaluated by immunohistochemistry (IHC). HER2 was evaluated by IHC and in situ hybridization (ISH). Results: We identified GAs in 11 of 57 cases (19%); 2 were bilateral and 9 were paired primary/recurrent BCs. The 11 cases included 1 primary, 1 primary/locally recurrent, and 9 primary/metastatic pairs. ER, PR, and HER2 status differed in 9 cases (16%), while AR status differed only in 3 (5%).16% 13/57 were negative for ER, PR, and HER2 (triple negative [TN]); of 9 TN BCs with GAs in paired primary/recurrent BCs, 6 of 9 (67%) were TN on both primary and recurrent disease (p = 0.0135). TP53 GAs were identified in 5 of the 11 cases (including the 2 synchronous), PIK3CA GAs were identified in 4 (1 synchronous), and PTEN GAs were identified in 3 (1 synchronous) cases. Other genes in which GAs appeared in only one of the pairs included CDH1 (synchronous), cMET and KRAS (Primary/recurrent pair). Of the 2 synchronously profiled cases, 1 had 2 and 1 had 3 different GAs in the bilateral BCs, and 2 GAs in both BCs. In the primary/metastatic pairs, all discordant GAs were wild type in the primary and pathogenic in the metastasis. Conclusions: We identified that common GAs differ in both synchronous primary BCs and in paired primary/metastatic tissues. Such discordance could influence treatment recommendations. These findings highlight the molecular evolution of BC and the importance of evaluating predictive markers of treatment benefit both in synchronous and metastatic BCs.