Background: There are limited large prospective single institution studies on outcome of breast cancer in patients with germline BRCA1 and BRCA2 mutation. The primary aim of this study was to determine the effect of a germline BRCA1 or BRCA2 mutation on recurrence-free survival (RFS) and overall survival (OS) in patients with breast cancer. Methods: This is a prospective cohort study of patients with invasive breast cancer recruited from the UT MD Anderson Cancer Center Breast Medical Oncology and Clinical Cancer Genetics Center. For the purpose of this analysis, newly diagnosed breast cancer patients who have had germline BRCA1 and BRCA2 testing within 12 months were included. Clinical and pathological data, and data regarding outcomes were collected in this prospective cohort. The Kaplan-Meier method and corresponding log-rank test were used to estimate OS and RFS and to compare survival by mutation status. Results: Between 1996 and 2015, 3026 patients were recruited. Median age at diagnosis was 45 (19-87) years. A germline BRCA mutation was detected in 361 (11.9%) patients (207 with BRCA1, 154 with BRCA2). After a median follow-up time of 5.3 (0.04-20.7) years, 437 (14.4%) patients recurred and 340 (11.2%) were deceased. At median follow-up time 5 years, 79.3% of BRCA1, 91.4% of BRCA2 and 89.6% of BRCA negative patients were disease free; this difference was significant (p = 0.0001). Difference in OS between BRCA1/2-positive and BRCA-negative patients was also significant (p = 0.0001), with 81.2% of BRCA1, 93.4% of BRCA2 and 90% of BRCA negative patients being alive at 5 years. Amongst 600 patients with triple negative breast cancer (TNBC) patients, DFS and OS were not significantly different between the 3 groups. Of those patients diagnosed under 40 years (n = 937), RFS and OS was significantly different between 3 groups at 5 years (0.001 for RFS and OS); 75% BRCA1, 92% BRCA2 and 86% BRCA negative patients were disease free and 77% BRCA1, 94% BRCA2 and 88% BRCA negative patients were alive. Conclusions: Patients with BRCA1 or BRCA2 mutations have different survival outcomes. The prognosis of the first cancer needs to be taken into consideration when deciding for preventive surgeries to prevent second primary breast cancers in these patients. Furthermore, for BRCA1 mutation carriers more effective therapy strategies need to be evaluated to improve outcome.