To examine the application of DNA microarray in drug discovery and development, cluster analysis for genome-wide expression data was tested after Saccharomyces cerevisiae was treated with nine antifungal agents with known and unknown pharmacological mechanisms. The results indicated that antifungal agents with similar action mode were clustered together. Amphotericin B and nystatin, ketoconazole and clotrimazole have been known to have similar antifungal mechanism respectively. Consistent with their known mechanisms, amphotericin B and nystatin were clustered together; also ketoconazole and clotrimazole were clustered together based on their expression patterns. Solasodine, which was known to inhibit the synthesis of ergosterol, had a close clustering position with ketoconazole and clotrimazole group. Analyzing the relationship among the known and unknown drugs using cluster approach, It can be infered that the pharmacological mechanisms of unknown drugs from their clustering positions relating to the known drugs.