Hair samples are increasingly used for measuring the long-term stress mediator cortisol. However, hair is not always available and nails (finger or toe), as a keratinized matrix, may be an alternative to hair. In order to measure cortisol and cortisone in the nail matrix, an LC-MS/MS method has been developed and validated using 13C3-labeled surrogate analytes. Both analytes were measured in ESI negative mode as formic acid adducts. Different sample preparation techniques were assessed, and single-step extraction in methanol was established for determination of cortisone and cortisol in the nail matrix. The method was successfully validated with limits of detection (LOD) and limits of quantification (LOQ) of 0.5 and 1.0 pg/mg for cortisol and cortisone, respectively. The calibration curve was linear up to a concentration of 500 pg/mg. Recovery was good for both analytes and showed values over 50%. Matrix effects with ion suppression occurred for both substances but could be corrected by the use of internal standard. Accuracy and precision were in the accepted range of ± 20% for both substances. The method was successfully applied to determine cortisol and cortisone concentrations in authentic nail samples. Cortisol and cortisone concentrations varied significantly among different fingernails, being highest in the little fingernails and lowest in the thumbnails. It could be shown that even in only 1 mg nail sample cortisol and cortisone can be reliably quantified. No correlation between hair and nail cortisol and cortisone concentrations could be found. Furthermore, cortisol and cortisone concentrations were significantly higher in hair. Graphical abstract.