Characterizing the crystallinity in PEEK is critical, since it dictates the mechanical behavior of the polymer. Wide angle X-ray scattering (WAXS) has been typically employed for this purpose; yet, it is impractical for the measurement of some composite materials. Differential scanning calorimetry (DSC) has also been used but with limited accuracy. Fourier transform infrared (FTIR) microscopy has been identified as a suitable method to measure the crystallinity of industrial grade PEEK, but its usefulness with medical grade PEEK remains unknown. By comparing FTIR, WAXS and DSC for a range of medical PEEK grades, we demonstrate that FTIR can detect changes in crystallinity due to annealing treatments and incorporation of carbon fibers or radiopaque compounds.