Presently appearance of resistance to antifungal agents among Aspergillus species is dramatically increasing. The objective of this study was to look at the in vitro activities of antifungal drugs against Iranian clinical (from nail, bronchoalveolar lavage, paranasal sinus) isolated A. flavus strains. The susceptibility of 45 aflatoxigenic and non-aflatoxigenic Aspergillus flavus strains were evaluated to six antifungal agents (caspofungin, itraconazole, amphotericin B, ketoconazole, fluconazole, nystatin) using CLSI M38-A2 broth microdilution method. The results indicated that 57.1%, 28.6% of aflatoxigenic and 25.8%, 6.5% of non-aflatoxigenic isolates were susceptible to caspofungin, amphotericin B respectively. All isolates but one aflatoxigenic strain were sensitive to ketoconazole. All 45 strains showed to be resistant to nystatin. Also 64.28%, 92.9% of aflatoxigenic and 64.51%, 100% of non-aflatoxigenic isolates were resistant to fluconazole and itraconazole in ranking order. There was no statistically significant difference between the susceptibilities of aflatoxigenic and non-aflatoxigenic strains of A. flavus to tested antifungal agents.