This study describes the physico-chemical properties and the skin permeation profile of quercetin (Q) and 3-O-methylquercetin (MQ) from lipid nanoemulsions. Formulations composed of octyldodecanol, egg lecithin, water (NE) and cetyl trimethyl ammonium bromide (CNE) were obtained by spontaneous emulsification. This procedure yielded monodisperse nanoemulsions exhibiting a mean droplet size of approximately 200-300 nm. Nanoemulsions were further characterized in terms of zeta-potential, surface tension, and morphology by transmission electron microscopy. The amount of flavonoids incorporated into nanoemulsions reached nearly 100% (at 1 mg/mL). The permeation studies were carried out using ear pig skin mounted in Franz diffusion cells. The overall results have shown a slow permeation profile of both Q and MQ from nanoemulsions. However, a higher permeation flux rate of flavonoids from CNE (approximately 0.2 microg/cm2/h) as compared to NE (approximately 0.08 microg/cm2/h) was observed, showing the effect of the positively charged surface of CNE on this parameter. Such results open interesting perspectives for the topical administration of the flavonoids Q and MQ.