OBJECTIVE: To describe the length of stay, the drug treatment costs and the diagnosis and therapeutic tests costs in patients hospitalized with a serious fungal infection and to analyze the factors associated to them. METHODS: A retrospective review of the clinical records of 399 hospitalization episodes which included a diagnosis of systemic mycosis going into 17 Spanish hospitals have been performed. The length of stay has been described as global and by the type of pathogen (aspergillosis, candidemia, emphirical and other pathogens), drug treatment costs and diagnosis tests. A descriptive analysis of the costs is performed. RESULTS: The average length of stay of the patients under study was 38,87 days. The average length of the antifungal treatment was 19,93 days, with 15,42 for intravenous treatment and 4,49 days for oral therapy. Candidemia represented the 42,6% of the sample, 17,3% was for aspergillosis, 34,1% for empiric treatment, and the resting 6% for other fungal infections. Amphotericin B was prescribed in 11,6% of the patients (with or without adding azoles), Amphotericin B lipid complex in 16,8%, Amphotericin B lisosomal in 23,6%, and exclusively Azoles in 29,3%. 9,2% of episodes were treated with a combination of conventional amphotericin B with the lipid or liposomal formulation, and a 3,8% a combination of these last two. Average cost of antifungal therapy was €4.240,39 (€2.838,87 to €5.641,91), with a wide variety between hospitals, determined by the type of antifungals prescribed. People aged over 65 years old (and occasionally people under 16 years old) showed shorter average days of total treatment, intravenous and oral. Transplanted and immunocompromised patients showed a longer time of treatment, and those with previous corticotherapy showed longer stays. CONCLUSIONS: The cost of hospital antifungal therapy is high and it is determined by the type of antifungal selected. Clinical characteristics of patients may influence the total cost of the treatment and/or the length of stay.