Zygomycoses are very rare invasive fungal infections (IFI). They primarily occur in the immunocompromised patients and are associated with a high mortality. During the last years, a rising incidence of zygomycosis in patients undergoing allogeneic haematopoietic stem cell transplantation (HSCT) has been reported, which is probably a part of the trend in the incidence of mould infections that has been going on for decades. Difficulty in diagnosis, especially concerning the differentiation of zygomycosis from the far more common aspergillosis, additionally hampers a reliable assessment of the incidence of zygomycosis. In patients undergoing allogeneic HSCT, changes in the frequency, severity and management of Graft-versus-Host-Disease (GvHD) also favour mould infections, among them zygomycosis. In centres employing voriconazole for prophylaxis of IFI since its approval for treatment in 2001, incidence of aspergillosis has markedly dropped. The assumption that the frequency of zygomycosis has increased since the introduction of voriconazole is not found in prospective trials and therefore needs verification, especially when considering the long ongoing trends in fungal incidence. Currently recruiting multicentre trials on primary prophylaxis of IFI will have to show the preventive effectiveness of antifungals with mould activity and the incidence of zygomycosis under prospectively controlled conditions.