Fluorescence Correlation Spectroscopy (FCS) offers the possibility to measure molecular interactions between active compounds and drug delivery systems such as cationic peptides or polymeric nanoparticles. In order to investigate the potential of FCS for drug carrier design, a complex made of protamine, a cationic peptide, and a 19mer oligonucleotide was characterised. Protamine was used to form proticles, agglomerates consisting of the oligonucleotide and the cationic peptide. The binding kinetics and proticle formation was studied by FCS. Complete binding of the oligonucleotide to protamine was achieved at a 1:2.5 (w/w) ratio. From the diffusion coefficient, D, a mean value for the hydrodynamic diameter was calculated at 53 nm, which was in agreement with data obtained from photon correlation spectroscopy (PCS). Oligonucleotide loading into cationic monomethylaminoethylmethacrylate (MMAEMA) nanoparticles was also determined by this method at 5.6% (5.6 microg per 100 microg of nanoparticles).