Amphotericin B (AMB) is the most widely used polyene antifungal drug for the treatment of systemic fungal infections, including invasive aspergillosis. It has been our aim to understand the molecular targets of AMB in Aspergillus fumigatus by genomic and proteomic approaches. In transcriptomic analysis, a total of 295 genes were found to be differentially expressed (165 upregulated and 130 downregulated), including many involving the ergosterol pathway, cell stress proteins, cell wall proteins, transport proteins, and hypothetical proteins. Proteomic profiles of A. fumigatus alone or A. fumigatus treated with AMB showed differential expression levels for 85 proteins (76 upregulated and 9 downregulated). Forty-eight of them were identified with high confidence and belonged to the above-mentioned categories. Differential expression levels for Rho-GDP dissociation inhibitor (Rho-GDI), secretory-pathway GDI, clathrin, Sec 31 (a subunit of the exocyst complex), and RAB GTPase Ypt51 in response to an antifungal drug are reported here for the first time and may represent a specific response of A. fumigatus to AMB. The expression of some of these genes was validated by real-time reverse transcription-PCR. The AMB responsive genes/proteins observed to be differentially expressed in A. fumigatus may be further explored for novel drug development.Invasive aspergillosis, caused primarily by Aspergillus fumigatus, has emerged as the leading cause of mortality among immunocompromised patients with underlying hematological diseases or bone marrow transplantation (7, 38). Amphotericin B (AMB), a broad-spectrum fungicidal agent, has been widely used to treat patients with invasive aspergillosis. AMB is reported to be fungicidal (MFC/MIC Յ 4) against all A. fumigatus and Aspergillus flavus isolates but not on Aspergillus terreus isolates (25). Its therapeutic use is limited by its toxicity (nephrotoxicity, cytotoxicity, and hepatotoxicity, etc.) in the host (13) and development of resistance in fungal isolates (42). However, use of lipid formulations of AMB, administration by the inhalation route, and development of less toxic analogues have facilitated better therapeutic outcomes (35). In general, it is known that AMB intercalates with ergosterol of the fungal cell membrane and forms pores resulting in leakage of fungal cell components, which leads to death via osmotic collapse (15, 22).It also promotes oxidative damage to cell membranes through generation of reactive oxygen species (ROS) (43) and damage to DNA resulting in loss of cell viability, a characteristic of apoptosis (31).Earlier efforts reported genome-wide expression analysis to understand the mechanism of action and specific effects of AMB and other antifungal drugs on nonfilamentous fungal species, such as Saccharomyces cerevisiae and Candida albicans (1,24,46). However, in an earlier study of interaction of A. fumigatus with voriconazole (11), decreased mRNA expression of ergosterol biosynthesis genes was observed, which was in contrast with previous reports of S....