Background: Disparities in the quality of diagnosis and treatment of breast cancer in sex and gender minority (SGM) populations are largely undefined. Only 24% of studies funded by the National Cancer Institute capture data on sexual orientation, while only 10% capture data on gender identity. To address this gap, the National Academies 2020 Report calls for adding sexual orientation and gender identity (SOGI) to ongoing data collection efforts. This case-control study matching SGM patients with breast cancer to cisgender heterosexual controls is the result of linking SOGI data to the Stanford University Healthcare (SHC) Oncoshare breast cancer database, which integrates data from the electronic medical record (EMR) and California Cancer Registry. Methods: An initial database query across the SHC EMR was performed for charts containing SOGI terms in patients with breast cancer seen in SHC Oncology. 686 charts were identified for manual review and after eliminating false positives, the sample was reduced to 92 SGM patients, who were then matched by year of diagnosis, age, stage, ER-status, and HER-2 status to cisgender heterosexual controls within Oncoshare. Additional data on demographics, diagnosis, treatment, and relapse were then manually abstracted from the EMR. Results: The SGM cohort was comprised of 80% lesbians, 13% bisexuals and 6% transgender men. The median age at diagnosis across both groups was 49. SGM patients were 72% white, 4% Asian, 12% Black or Latinx 6% other compared to 63% white, 24% Asian, 6% Black or Latinx, 6% other in the controls (p = 0.0006). Thirteen percent and 32% of SGM patients engaged in risky alcohol and illicit drug use respectively, compared to 3% and 6% of controls (p = 0.028; p < 0.0001). Estrogen exposure risk factors including median age of menarche, first delivery, menopause, and use of exogenous estrogens were balanced between the two groups, but SGM patients had fewer children (median 0 vs 2, p < 0.0001). There was a delay in time to diagnosis from symptom onset in SGM patients versus controls (median 64 days vs 37 days, p = 0.043). There was no difference in surgical approach, use of post-lumpectomy radiation, or use of neoadjuvant chemotherapy for stage III disease. However, SGM patients were less likely to undergo chest reconstruction (55% vs 82%, p = 0.0098) and if ER+, to complete ≥5 years of ER-directed therapy (53% vs 72%, p = 0.048). SGM patients used more alternative medicine (46% vs 29%, p = 0.033) and had a higher rate of documented refusal of recommended oncologic treatments (38% vs 21%, p = 0.0088). Correspondingly, SGM patients experienced a higher recurrence rate (31% vs 14%, p = 0.0124). Conclusions: To our knowledge, this is the first study to examine quality of diagnosis and treatment of breast cancer in SGM patients. Several novel potential healthcare disparities are identified, which should be further evaluated in population-based studies to inform interventions.