We present an extensive theoretical and experimental study to identify the effect on the Raman spectrum due to interface interdiffusion between GaN and AlN layers in short-period GaN/AlN superlattices (SLs). The Raman spectra for SLs with sharp interfaces and with different degree of interface diffusion are simulated by ab initio calculations and within the framework of the random-element isodisplacement model. The comparison of the results of theoretical calculations and experimental data obtained on PA MBE and MOVPE grown SLs, showed that the bands related to A1(LO) confined phonons are very sensitive to the degree of interface diffusion. As a result, a correlation between the Raman spectra in the range of A1(LO) confined phonons and the interface quality in SLs is obtained. This opens up new possibilities for the analysis of the structural characteristics of short-period GaN/AlN SLs using Raman spectroscopy.