Secondary osteosarcoma from fibrous dysplasia (FD) is very rare. The etiology of FD is linked to activating missense mutations of the guanine nucleotide-binding protein alpha-subunit (GNAS) gene, which encodes the stimulatory alpha subunit of the G protein (G(s)alpha) and is located at chromosome 20q13. These mutations are central to the pathogenesis of FD; however, it is not known whether G(s)alpha mutations are retained following malignant transformation in FD. In addition, to the best of our knowledge, no studies have been performed on chromosomal analysis of secondary osteosarcoma from FD. The present study presents a case of secondary osteosarcoma arising from polyostotic FD in a 72-year-old male. Chromosomal analysis showed 44, X, -Y, add(4)(p11), add(5)(p15), der(11)add(11)(p15) t(1;11)(q21;q23), add(12)(q11), -13, der(22)t(12;22)(q11;p12). Reverse transcription-polymerase chain reaction (RT-PCR) analysis demonstrated the presence of a G(s)alpha mutation in both the primary tumor cells and secondary osteosarcoma cells. There was no alteration in this mutation in the region of malignant transformation, which suggests that this mutation may be a useful clinical marker for distinguishing de novo osteosarcoma (primary osteosarcoma) from secondary osteosarcoma arising from FD.