A combinatorial extraction method and an automated matrix-assisted laser desorption/ionization (MALDI) mass spectrometry procedure were used to improve the clinical analysis of the immunosuppressant drug cyclosporin A. Cyclosporin extracts from whole blood were analyzed by MALDI and electrospray ionization (ESI) mass spectrometry, allowing for their identification and quantification. Due to limitations associated with the current multistep cyclosporin extraction procedure from whole blood, a combinatorial approach was devised to optimize this extraction. Optimization was performed by generating an array of solvent systems to be used for extraction from blood, and an automated analysis was carried out on a MALDI mass spectrometer to identify successful extractions. The first generation of experiments revealed four binary solvent systems to be effective for cyclosporin extraction (hexane/EtOH, ACN/H2O, ACN/MeOH, and hexane/CHCl3). A new array based on these solvent systems was generated, and a second iteration of these experiments was then performed. In the second generation of experiments, hexane/CHCl3 (70:30) was found to provide the most effective single-step extraction of these solvent systems for cyclosporin and its metabolites. The limits of detection were determined to be 15 ng/mL in whole blood for ESI/MS and MALDI-MS and could also be used for identifying major drug metabolites. In addition to applying this combinatorial approach to extraction procedures, this experimental design could easily be extended to examine other approaches, such as optimizing chemical reactions and screening inhibitors in enzymatic reactions.