This paper describes characterization of lyophilized lipid nanocapsules loaded with Alexa 488 by fluorescence correlation spectroscopy (FCS). Fluorimetry analysis of nanocapsules containing self-quenching concentrations of 5- and 6-carboxyfluorescein was performed to establish a point of reference for FCS. FCS results complemented the results obtained by fluorimetry for a bulk nanocapsule solution and provided additional information about the size and dye retention by individual nanocapsules. Using this method, we determined that nanocapsules composed of the thiol-functionalized lipids showed the best dye retention and the most consistent results. Dye retention, size, and photolysis efficiency of these thiol-functionalized nanocapsules doped with a far-red photosensitizer did not change substantially upon lyophilization and storage at -20 degrees C for up to 2 months, making lyophilization a suitable method for the long-term storage of nanocapsules with the appropriate lipid composition.