This paper presents a study on the lattice dynamics of doped topological insulator (Cu,Ni)xBi2Se3 single crystals probed using Raman scattering spectroscopy. The single crystals were grown by melting and characterized through X-ray diffraction and scanning electron microscopy with energy dispersive X-ray spectroscopy. The diffraction patterns were indexed within the space group R-3m and the samples belonged to the rhombohedral layered structure group typical of Bi2Se3. A Raman scattering study was developed, in which three modes were observed at low frequencies: A1g1, Eg2 and A1g2. The low frequency Eg1 mode, even if theoretically predicted, was not observed. No difference was observed in Raman lines between the pure and (Cu,Ni)-doped samples, indicating that the Cu and Ni are probably intercalated (and not substituted) between the Se layers. •The samples are highly oriented with approximately 100 nm tick lamellas.•No difference was observed in Raman modes between pure and (Cu,Ni)-doped samples.•Cu and Ni were intercalated (and not substituted) between the Se layers.