A detailed Raman characterization of the structural properties of as-grown and annealed self-assembled Si/Ge dot multilayers is reported in this paper. Several new modes in as-grown or annealed Si/Ge dots and a frequency splitting of 4.2 cm(-1) between the longitudinal (LO) and transversal optical (TO) Ge-Ge modes in as-grown Si/Ge dots are observed in Raman spectra. An average Ge content of 0.8 and lateral strain of -3.4% are consistently obtained from these spectral features for as-grown Si/Ge dots with a lateral size of about 20 nm and a height of about 2 nm. It suggests that a certain amount of intermixing between Si spacer layers and Si/Ge dots takes place for the Si/Ge dot multilayers. The annealing behavior of the Ge-Si mode in Si/Ge dots indicates that the observed sharp Ge-Si mode is a Ge-Si alloy mode within the core regions of Si/Ge dots, rather than a Ge-Si interface mode in the interface regions of dots. The phonon strain-shift coefficients of the Ge-Ge and Ge-Si modes are determined for the small-sized Si/Ge dots with a high Ge content under a biaxial strain condition. The results show that the LO-TO frequency splitting of the Ge-Ge mode and the frequencies of the Ge-Ge and Ge-Si modes can be used as an efficient way to determine the average strain and composition in uncorrelated small-sized Si/Ge dot multilayers in which the mean strain field is close to the biaxial case.