The permeability of dithionite through bilayers was utilized to probe the structural defects in the bilayers of these lipids through their respective gel-fluid and bilayer-hexagonal phase transitions. The water soluble dithionite ion penetrates intact bilayers very slowly. The rate of irreversible quenching of the fluorescence of NBD-PE labelled liposomes may thus be used as an indicator of the permeability of this ion through bilayers. The quenching rate has a fast and a slow component, the fast one corresponds to the quenching of fluorophores immediately accessible to the quencher, i.e. those on the outer surface of liposomes. The slower component represents the averaged rate of penetration of the quencher through the bilayer, to quench those fluorophores at the inner shells of the multilamellar vesicles. Both rates may be approximated by a single exponential function. The slow exponent is simply related to the permeability. The permeability of DMPC as a function of temperature shows a peak at the gel-fluid phase transition at 24°C, but returns to about the pre-transition value at temperatures above the phase transition. The permeability of egg PE shows a hump at 45°C before the hexagonal phase transition at 65°C is reached and becomes infinite at the hexagonal phase transition as all fluorophores are immediately accessible to the quencher. We believe that the permeability measured by this method relates more to the molecular packing defects which maximizes at the gel-fluid phase transition temperature and at temperatures just below the bilayer-hexagonal phase transition, rather than the general packing order which simply changes with structural phases.