Invasive fungal infections (IFIs) continue to cause considerable morbidity and mortality in haematopoietic stem cell transplant recipients. The epidemiology of IFI has changed since the late 1980s, with a trend towards a reduction in invasive infection due to opportunistic yeasts and an increase in invasive mould infections, particularly by Aspergillus spp. Since the introduction of fluconazole for prophylaxis, the incidence rate of invasive candidiasis is close to 5% and the risk factors related to invasive candidiasis are gastrointestinal tract colonisation, cytomegalovirus disease and a prior episode of bacteraemia. The highest risk for invasive aspergillosis was observed in older patients and patients with graft-versus-host disease and immunosuppressive therapy, steroid use (>1-2 mg/kg/day), persistent neutropenia and certain types of transplantation (cord blood transplant, allogeneic mismatched or T-cell depletion). In those cases, rational preventive measures must be implemented and vigilance is necessary in order to diagnose infection as soon as possible.