FOP affects the neck, spine, chest, shoulders, elbows, wrists, hips, knees, ankles, jaw, and many areas in between. The progression of ossification follows a characteristic pattern. Usually extra bone forms in the neck, spine, and shoulders before developing in the elbows, hips and knees. The muscles of the diaphragm, tongue, eyes, face, and heart are characteristically spared. The well-documented and characteristic progression of FOP, as well as the regions not affected, likely hold important clues to the cause and development of the disease.

FOP affects mobility because the body's joints, such as the knees or the elbows, connect the bones and aid in movement. In FOP, extra bone replaces the ligaments (which cover the joints), as well as muscles and tendons (which move the joints). Consequently, movement in areas affected by FOP becomes difficult or impossible.