A comparative study between the specular reflectance and photoacoustic FTIR techniques is presented in this work. The potential and limitations of these two methods are investigated by following and analyzing structural variations that take place at the surface in annealed injection-molded polyamide 6,6. Both spectroscopic techniques appear to be quite sensitive in detecting small structural changes that occur in polyamide 6,6 when submitted to different annealing temperatures. However, the presence of distorted bands in the specular reflection spectra makes the photoacoustic FTIR method more attractive for the IR vibrational analysis of difficult materials (e.g., composites, black-filled polymers, paints, etc.) that cannot be easily characterized by conventional transmission FTIR.