Saccharomyces cerevisiae is widely used as a probiotic compound. Clinical data suggest that this agent is safe and effective. We report two cases of fungemia caused by S. cerevisiae occurring in immunosuppressed patients treated orally with S. boulardii Molecular typing confirmed clonality in isolate strains from patients and the capsule. Physicians caring for immunosuppressed patients must be aware of this potential serious complication of probiotic use.