OBJECTIVES: Comparing the cost-effectiveness of Micafungin and Caspofungin for the treatment of systemic candida infections (including invasive candidiasis and candidaemia) in Switzerland. METHODS: To this end, a health economic decision model, based on a phase-III double-blind RCT with global patient data is used. Hospitalization and primary medication costs are based on official Swiss data. The effectiveness outcome is defined as successfully treated and alive patients at the end of the study period. To test for robustness of cost-effectiveness results, a sub-group analysis, a two-way sensitivity analysis and a probabilistic sensitivity analysis (PSA) are performed. RESULTS: The main analysis shows that 60 % of Micafungin patients were successfully treated and survived at the end of study compared to 58 % of Caspofungin patients. The costs of a Micafungin treatment (CHF 54,503) are smaller than the costs of a Caspofungin treatment (CHF 56,704). This results in a lower cost-effectiveness ratio for Micafungin (CHF 91,356) than for Caspofungin (CHF 98,900). Moreover, Micafungin dominates Caspofungin in the incremental cost-effectiveness analysis. For European patients only, who can be assumed to be a more homogenous group and a better approximation of Swiss patients, the cost-effectiveness ratio for Micafungin is CHF 88,474 compared to CHF 105,202 for Caspofungin. Two-way sensitivity analyses for both, total sample and European sub-sample, render Micafungin more cost-effective than Caspofungin in 20 out of 20 scenarios (highest incremental cost-effectiveness for Micafungin amounts to CHF 16,382). Probabilistic sensitivity analysis shows similar findings. CONCLUSIONS: This study analyzes the cost-effectiveness of Micafungin as compared to Caspofungin for the treatment of systemic candida infections in Switzerland. Both lower costs and higher effectiveness of Micafungin render Micafungin as more cost-effective than Caspofungin.