Measuring cyclosporine A (CsA), an immunosuppressive drug used to prevent heart transplant rejection, concentrations in myocardial biopsies might be more informative than its measurement in whole blood. Therefore, a fast, accurate and reproductive method to determine CsA concentration in this complex matrix is needed. We report the validation of a liquid chromatography tandem mass spectrometry method to measure CsA concentration in heart parenchyma, applicable to everyday practice. The method was found to be precise, accurate, reproducible, specific of CsA, and without any matrix effect or carry-over. The lower limit of quantification was 50 pg of CsA in myocardium. The method was linear up to 2000 pg of CsA in myocardium. Samples were found stable for one year at -80°C. At last, 40 drugs which could be prescribed to heart transplant recipients were tested with the method and showed no interference with CsA signal. The method was suitable to quantify CsA in endomyocardial biopsies from heart transplanted patients. This method allows designing clinical studies aiming at exploring the relationship between CsA intra-graft concentrations and outcome.Abbreviations: acute rejection (AR); adverse events (AE); centre de ressources biologiques (CRB); coefficient of variation (CV); cyclosporine A (CsA); European Medicine Agency (EMA); endomyocardial biopsies (EMB); heart transplantation (HT); high performance liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS); immunosuppressive drugs (ISD); interleukine-2 (IL-2); internal standard (IS); lower limit of quantification (LLOQ); mass spectrometry (MS); matrix factor (MF); peripheral blood mononuclear cells (PBMC); quality controls (QC); relative error (RE); standards (Std); therapeutic drug monitoring (TDM).