This retrospective study of 251 lung transplant patients aimed to determine the prevalence, clinical presentation and mortality of Aspergillus infection in order to define specific risk factors and to compare survival in patients with and without infection. Aspergillus was isolated from 86 (33%) cases, which involved colonisation (n = 50), tracheobronchial lesions (n = 17) or invasive aspergillosis (n = 19). Overall, aspergillosis had an impact on survival (p < 0.05); in fact the 5-year mortality rate was substantially higher in single lung transplant recipients with bronchial anastomotic infection, and in those with late-onset infections and chronic rejection. A significant association (p < 0.05) was found between acute rejection and the time at which fungal infection was diagnosed. Aspergillus infection was not related to cytomegalovirus infection or treatment with corticosteroids. The mortality rate for invasive infections was 78% and was related to survival (p < 0.0001); invasive aspergillosis was also associated with chronic rejection (p < 0.05), but not with high corticosteroid doses (p 0.49) or use of tacrolimus (p 0.73). In conclusion, Aspergillus infection was associated with a reduction in the 5-year survival rate of lung transplant recipients, and this was particularly true for patients infected with the invasive forms and for patients with single lung transplants, bronchial anastomotic infection and chronic rejection. Isolation of Aspergillus spp. from respiratory samples preceded acute rejection, and may be a marker of graft dysfunction and/or airway inflammation. Close monitoring, or even pre-emptive antifungal therapy, is recommended for patients with chronic rejection or bronchial airway mechanical abnormalities and persistent Aspergillus colonisation.