Multilayer films containing α- and β-casein and polypeptides, poly-L-lysine (PLL), and poly-L-arginine (PLArg) were formed by the layer-by-layer technique and Fourier Transform InfraRed spectroscopy with Attenuated Total Reflection (FTIR-ATR) and FTIR/Grazing Angle analyzed their infrared spectra. We investigated the changes of conformations of casein and polypeptides in the complexes formed during the build-up of the films. To elucidate the differences in the mechanism of complex formation leading to various growths of (PLL/casein)n and (PLArg/casein)n films, we performed the molecular dynamics simulations of the systems consisting of short PLL and PLArg chains and the representative peptide chains-casein fragments, which consists of several aminoacid sequences. The results of the simulation indicated the preferential formation of hydrogen bonds of poly-L-arginine with phosphoserine and glutamic acid residues of caseins. FTIR spectra confirmed those, which revealed greater conformational changes during the formation of casein complex with poly-L-arginine than with poly-L-lysine resulting from stronger interactions, which was also reflected in the bigger growth of (PLArg/casein)n films with the number of deposited layers.