Pulmonary hamartoma is a benign neoplasm that rarely recurs or undergoes malignant transformation. Herein, we report a 48-year-old woman with a history of an incomplete excised nonchondroid pulmonary hamartoma presenting as an indolent tumor recurrence. Excision of the tumor revealed a well-differentiated liposarcoma arising from the hamartomatous component. Fluorescence in situ hybridation analysis for HMGA2 and MDM2 was performed on both hamartomatous and liposarcomatous component. MDM2 and HMGA2 amplification were found in a subset of stromal cells in the hamartomatous component and in most cells of the well-differentiated liposarcoma. No rearrangement HMGA2 was found in the pulmonary hamartoma component. These findings suggest that the formation of the 12q14-q15 chromosome amplicon, the characteristic cytogenetic finding of well-differentiated liposarcomas and the structural genomic component of the supernumerary ring and giant rod chromosomes, occurred before the morphologic changes characteristic of these malignant adipose tissue tumors and likely represents a very early molecular event in their development.