The crystallinity degree of thin polyamide films (PA66, 610 and 612) spin coated on four types of substrates are estimated. Two original methods based on the analysis of infrared spectra are proposed. The high sensitivity of polarization modulation reflection-absorption spectroscopy for the study of thin polymer films leads to quantitative results. These two methods offer the possibility to estimate the degree of crystallinity by using infrared spectroscopy, independently of any other technique, if the crystallinity degree in the isotropic bulk state is known. Polyamides are spin coated, on the one hand, on inert and highly reflecting gold substrates, and on the other hand, on the same gold substrates grafted with different chemical functionality. Our calculations show a lower crystallinity degree for inert substrate and higher values for functionalized systems with respect to the bulk. These results suggest that the surface chemical grafts not only play the role of nucleation seeds, but also affect the crystalline morphology as seen by atomic force microscopy.