A high‐performance liquid chromatography (HPLC) method for assay of d‐Lys6–GnRH contained in a microemulsion‐type formulation is described. The peptide is extracted from the microemulsion matrix and quantified using a two‐step gradient method. Separation from microemulsion compounds and potential peptide oxidation products was achieved on a Jupiter C18 column at 40°C, using a gradient of 10–35% CH3CN for peptide elution. The correlation of peak intensity measured at 220 nm and peptide concentration was linear over the range 2.5–60 µg/mL with a correlation coefficient of 0.9997 and a y‐intercept not significantly different from zero (p > 0.05). Intraday and interday variability of the assay was less than 5% for multiple injections of samples containing 7.5, 30 and 60 µg/mL. The lower limit of quantitation was calculated to be 0.38 µg/mL, and the lower limit of detection was 0.13 µg/mL. The assay was applied to samples that were stressed under physiological conditions (37°C, pH 7.4) over 4 days. Three degradation peaks were well resolved from the parent peptide, demonstrating the selectivity of the assay. Off‐line MALDI TOF mass spectrometry was applied to identify these degradation species as oxidation products of the peptide. Copyright © 2009 John Wiley & Sons, Ltd.