Deep fungal infections (FI) were diagnosed in 27 out of 209 consecutive bone marrow transplantation (BMT) recipients. Autopsy verified that the incidence of deep FI was 10% and the overall incidence was 13%. Using bivariate logistic regression analysis at the time of BMT, high recipient age (p = 0.003), low bone marrow cell dose (p = 0.007), recipient cytomegalovirus (CMV) seropositivity (p = 0.009) and splenectomy (p = 0.03) were significant risk factors for deep FI. In multivariate analysis, splenectomy (p = 0.008), recipient CMV seropositivity (p = 0.01) and low bone marrow cell dose (p = 0.01) held as significant. At 30 days post-BMT anti-thymocyte globulin treatment (p = 0.0006) and graft-versus-host disease grade II-IV (p = 0.005) were significant risk variables in bivariate logistic regression analysis and Fisher's exact probability test. Patients with these risk factors are candidates for treatment with antifungal drugs when they suffer from leukopenia and unclear fever.