Delayed recovery of the immune system is a major cause of post-transplant infection. Natural interferon (IFN)-alpha/beta-producing cells (IPC) appear to play a critical role in inducing effective immune responses to a variety of microbial pathogens by producing an enormous amount of IFN-alpha/beta and thereafter by differentiating into dendritic cells. Here, we examined the recovery of IPC as well as other immune cells in 28 patients after allogeneic hematopoietic stem cell transplantation (HSCT) in order to investigate the role of IPC in post-transplant immune reconstitution. In uncomplicated cases, IPC frequency recovered to the lower range of normal values within 30 days after transplantation, resembling the prompt recovery of other cell types in innate immunity. In contrast, the recovery of IPC was profoundly suppressed in the cases with acute graft-versus-host disease (GVHD) and glucocorticoid administration. The patients with lower numbers of IPC were significantly more susceptible to viral infection. The prompt recovery of IPC in uncomplicated cases may contribute to establishing a first line of host defense at the early stage after allogeneic HSCT, whereas the marked suppression of IPC recovery accompanying acute GVHD and glucocorticoid administration may increase the risk of opportunistic infections.