A selective and sensitive polar-reversed phase LC method was validated for simultaneous quantification of the main Achyrocline satureioides flavonoids (quercetin, luteolin, and 3-O-methylquercetin) in skin samples after permeation/retention studies from topical nanoemulsions. The method was linear in a range of 0.25 to 10.0 microg/mL exhibiting a coefficient of determination higher than 0.999 for all flavonoids. No interference of the nanoemulsion excipients or skin components was observed in the retention times of all flavonoids. The R.S.D. values for intra- and inter-day precision experiments were lower than 6.73%. Flavonoids recovery from nanoemulsions and skin matrices was between 90.05 and 109.88%. In a permeation/retention study with porcine ear high amount of 3-O-methylquercetin was found in the skin sample (0.92 +/- 0.22 microg/g) after two hours. The proposed method was suitable to quantify the main flavonoids of A. satureioides in skin permeation/retention studies from topical nanoemulsions.