The results of joint theoretical and experimental studies aimed at revealing features in the Raman spectra, which can be used for evaluation of the interface quality between GaN and AlN layers in short-period GaN/AlN superlattices (SLs) are presented. The Raman spectra for SLs with sharp interface and with different degree of interface diffusion are simulated by ab initio calculations and within the framework of random-element isodisplacement model, respectively. The comparison of the results of theoretical calculations and experimental data obtained on PA MBE and MOVPE grown SLs, leads to conclusion that the spectral region of the A1(LO) confined phonons is very sensitive to the degree of interface sharpness. As a result of comprehensive studies, the correlations between the parameters of the A1(LO) confined phonons and the structure of SLs are obtained. The results of the complex studies can be used to optimize the parameters of the growth process in order to form structurally perfect short-period GaN/AlN SLs.