During the period January 2004 to April 2007, nine cases of breakthrough invasive aspergillosis occurred among 156 allogeneic haematopoietic stem cell transplant recipients receiving caspofungin therapy, mainly for empirical treatment of persisting fever. Voriconazole salvage therapy induced two complete responses. However, seven patients ultimately died a median of 5 weeks after diagnosis, including five patients with aspergillosis. This high incidence of breakthrough invasive aspergillosis in this patient population receiving caspofungin therapy warrants further investigation.