Lipomatous lesions rarely involve the bronchial tree, and detailed morphologic and molecular cytogenetic analysis of these tumors is lacking. The clinicopathologic features of 12 endobronchial lipomatous neoplasms were studied, with ancillary fluorescence in situ hybridization performed in subsets of cases for CPM, which is amplified in atypical lipomatous tumors/well-differentiated liposarcomas (ALT/WDL), and HMGA1 and HMGA2, which are often rearranged in lipomas. The cases occurred predominately in older men (91%) (age range 44 to 80 y, mean 65 y). Most patients (80%) had a former or current history of heavy smoking (20 to 100 pack-years). Three patients had concurrent pulmonary squamous cell carcinoma, and 1 had a history of multiple lung cancers. Most lesions were small (<2.5 cm) and discovered incidentally. A subset of tumors showed atypical morphologic features that would be suggestive of ALT/WDL in soft tissue sites, including regions of fibrosis and scattered hyperchromatic stromal cells. However, all cases with atypia were CPM negative and behaved in a clinically benign manner. Seven cases were tested for HMGA1 and HMGA2 rearrangement; 4 showed HMGA2 rearrangement, and 1 showed HMGA1 rearrangement, consistent with lipomas. Two cases were negative for HMGA1/2 rearrangements. We conclude that endobronchial lipomatous neoplasms represent lipomas, even in the presence of morphologic features suggestive of ALT/WDL. Ancillary fluorescence in situ hybridization testing may be very valuable in the analysis of these rare tumors, as true ALT/WDL seem to be very rare or nonexistent at this anatomic site.