Background: Thymoma (T) and thymic carcinoma (TC) are the most common malignancies of the anterior mediastinum. Additionally, thymoma has an unique association with autoimmune disorders, notably myasthenia gravis (MG). Histologic classification of TETs has been largely based on the gross description of the epithelial cell appearance and the relative abundance of associated lymphocytes. A comprehensive molecular analysis of TETs has not heretofore been conducted. Methods: The TCGA Research Network conducted multi-platform analyses of 117 TETs (T = 105; TC = 10 and micronodular T = 2), which included whole-exome, transcriptome, methylome and targeted proteome analysis. Patient characteristics: median age = 60 years (range 17-84); M:F (%) = 52:48; Masaoka Stage (I-36, IIA-39, IIB-19; III-15; IVA-1; IVB-5); mg was present in 32 patients. No patient had prior therapy for metastatic disease, but 14 had prior chemotherapy and 39 had prior radiation therapy in adjuvant setting. WHO histologic classification (blinded review) revealed A = 10; A/B = 48, B1 = 12, B2 = 25, B3 = 10, micronodular T = 2 and TC = 10. Results: T has one of the lowest mutational loads of any tumor in the TCGA. A unique transcription factor, GTF2I, was the most commonly observed mutation in WHO Types A and A/B. All GTF2I mutations were exclusively at the amino acid 424 locus. This is the only tumor with this specific mutation within the entire TCGA database. HRAS, NRAS and TP53 mutations were less commonly noted among all TETs. Four distinct molecular-driven subtypes of TETs were identified that strongly correlated with the current WHO histologic classification. Increased aneuploidy and overexpression of muscle auto-antigens were associated with mg phenotype. Conclusions: Based on molecular analysis, four clusters were identified that correlated strongly with the current WHO Histologic Classification. Also identified was a unique mutation in GTF2I, which was associated with WHO Type A and A/B thymoma. This international effort represents the largest and most comprehensive molecular analysis of TETs conducted to date is expected to have important clinical and translational implications for this rare disease.