FT Raman spectroscopy has been applied to determine the location of PRODAN within HDL and to investigate its influence on the structure of the particle. The complex spectra of HDL and HDL labeled with PRODAN were divided into three regions according to the wave numbers, and adherent spectra were compared separately. Additionally, recorded spectra of protein and lipid fractions of HDL were used as a support for the assignment of particular vibrations in intact particles. In high frequency region, the shift in vibrational frequencies of CH3 groups but almost negligible shift of CH2 groups suggests that PRODAN is situated at the water/lipid interface in the vicinity of the protein. The statement is supported by the observed influence of PRODAN on particular lipid vibrations of phospholipids head-groups. In the fingerprint region, the influence of PRODAN is observed as the slight change in beta-strand secondary structure of apolipoprotein and strongly reduced vibrations of the acyl chain in lipids. That additionally confirms that PRODAN mainly interacts with the lipid domain of the particle. In the low frequency region, the lack of change in Tyr Fermi resonance doublet and only slight differences in the pattern of CS and SS stretching vibrations in labeled HDL confirms that PRODAN has no influence on structure of apolipoprotein embedded in lipid domain. The main conclusions drawn from the vibrational spectra of HDL with and without PRODAN clearly confirm that PRODAN induces negligible changes in HDL structure and hence is reliable fluorescent label for the structural analysis.