Fibrodysplasia ossificans progressiva (FOP) is a rare genetic disease with a progressive course characterized by episodically local flare-ups, which often but not always leads to heterotopic bone formation (HO). Recently, we showed that [18F]NaF PET/CT may be the first tool to monitor progression of a posttraumatic flare-up leading to new HO, which was demonstrated in a patient with FOP who underwent a maxillofacial surgery. This paper evaluates [18F]NaF PET/CT as a marker of FOP disease activity, comparing its use with other imaging modalities known in literature. In addition, the follow-up of a spontaneous flare-up in a 19-year old patient is presented showing high muscle [18F]NaF uptake in one defined part within the flare-up area after three weeks. During follow-up [18F]NaF PET /CT scan revealed newly formed heterotopic bone but only in this previously active [18F]NaF region. In conclusion, increased muscle [18F]NaF uptake may predict future HO development in FOP patients. At present [18F]NaF PET/CT appears to be a sensitive imaging modality to serve as a noninvasive marker for bone formation and to monitor disease activity during flare-ups in FOP.