By CLSI interpretive criteria, anidulafungin and micafungin MICs determined by various methods were sensitive (60 to 70%) and highly specific (94 to 100%) for identifying FKS mutations among 120 Candida glabrata isolates. Anidulafungin and micafungin breakpoints were more specific than CLSI's caspofungin breakpoint in identifying FKS mutant strains and patients with invasive candidiasis who were likely to fail echinocandin treatment (P ≤ 0.0001 for both). Echinocandin MICs were most useful clinically when interpreted in the context of prior echinocandin exposure.