Annealing of poly(etheretherketone) PEEK, has been studied for two materials cold crystallized from the rubbery amorphous state. The first material is a low molecular weight PEEK; the second is commercially available neat resin. Differential scanning calorimetry was used to monitor the melting behavior of annealing samples. The effect of thermal history on melting behavior is complex and depends upon annealing temperature, residence time at the annealing temperature, and subsequent scanning rate. Thermal stability of both materials is improved by annealing, and for an annealing temperature near the melting point, the polymer can be stabilized against reorganization during the scan. Variations of density, degree of crystallinity, and X-ray long period were studied as a function of annealing temperature for the commercial material. Wide angle X-ray scattering was used to study the structure of annealed PEEK. An additional scattering peak was observed at higher d-spacing when annealed samples were cooled quickly.