Recent studies have shown the effect of soy isoflavones in preventing skin photoaging and photocarcinogenesis, especially for genistein (GEN). Nanoemulsions have been proposed as a delivery system for GEN administration due to the low water solubility of this isoflavone. This article describes the validation of an isocratic liquid chromatography method to determine GEN in porcine ear skin layers from nanoemulsions before and after incorporation into hydrogels. The analyses are performed on a reversed-phase C18 column using a mobile phase composed of methanol-water (70:30, v/v) under acid conditions (at pH 3.0) and UV detection at 270 nm. The method is linear in the range of 0.1-10 µg/mL (r(2) > 0.999) in the presence of skin extracts. The low limit of quantitation is estimated as 0.1 µg/mL. No interferences from formulation excipients or skin layer compounds are detected. The RSD values for intra- and inter-day precision are lower than 15%. Recovery ranged from approximately 90% to 110%. The method is applied to estimate GEN retention in the skin from formulations using Franz diffusion cells. The highest amount of GEN is detected in the epidermis (185 µg/cm(2)). In conclusion, the method proved to be specific, precise, and accurate in determining GEN amounts from formulations in skin retention studies.