Candida albicans frequently develops resistance to treatment with azole drugs due to the acquisition of gain-of-function mutations in the transcription factor Tac1p. Tac1p hyperactivation in azole-resistant isolates results in the constitutive overexpression of several genes, including CDR1 and CDR2, which encode two homologous transporters of the ATP-binding cassette family. Functional studies of Cdr1p and Cdr2p have been carried out so far by heterologous expression in the budding yeast Saccharomyces cerevisiae and by gene deletion or overexpression in azole-sensitive C. albicans strains in which CDR1 expression is low and CDR2 expression is undetectable. Thus, the direct demonstration that CDR1 and CDR2 overexpression causes azole resistance in clinical strains is still lacking, as is our knowledge of the relative contribution of each transporter to clinical azole resistance. In the present study, we used the SAT1 flipper system to delete the CDR1 and CDR2 genes from clinical isolate 5674. This strain is resistant to several azole derivatives due to a strong hyperactive mutation in Tac1p and expresses high levels of Cdr1p and Cdr2p. We found that deleting CDR1 had a major effect, reducing resistance to fluconazole (FLC), ketoconazole (KTC), and itraconazole (ITC) by 6-, 4-, and 8-fold, respectively. Deleting CDR2 had a much weaker effect, reducing FLC or KTC resistance by 1.5-fold, and had no effect on ITC resistance. These results demonstrate that Cdr1p is a major determinant of azole resistance in strain 5674 and potentially in other clinical strains overexpressing Cdr1p and Cdr2p, while Cdr2p plays a more minor role.Candida albicans is one of the leading causes of fungal infections affecting immunocompromised individuals. Candida infections range from chronic superficial infections of the skin and mucosal surfaces to invasive, life-threatening systemic infections (21, 38). Many antifungal drugs used to treat Candida infections target the biosynthesis of ergosterol, the major sterol in the fungal cell membranes (24). Polyenes, such as amphotericin B (AMB), directly bind to ergosterol and form pores in the cell membrane, resulting in low selectivity and high toxicity (24). Azoles, a class of well-tolerated antifungal drugs that includes fluconazole (FLC), ketoconazole (KTC), itraconazole (ITC), and new-generation derivatives such as voriconazole and posaconazole, target the enzyme lanosterol 14␣-demethylase (Erg11p), which is involved in ergosterol biosynthesis, blocking the production of ergosterol and causing the accumulation of toxic intermediate sterol species (24). As a consequence, the fluidity and permeability of the fungal cell membrane are changed and the activity of membrane-bound proteins, such as enzymes involved in cell wall synthesis, is altered (24).However, the fungistatic rather than fungicidal action of azole drugs leads to the frequent emergence of azole-resistant (A r ) C. albicans strains (1, 44). One mechanism of azole resistance consists of increased levels of ERG11 RNA, resulting in i...