Acquired aplastic anemia (AAA) is a disorder with multiple causes. The pathogenetic mechanisms leading to marrow failure are diverse. The clinical finding, that most patients respond to immunosuppressive therapy implicates an immune pathophysiology of AAA. On the other hand successful and long lasting reconstitution after allogeneic stem cell transplantation implicates, that a stem cell defect is a major pathogenetic factor. We analyzed immunological and hematological parameters on 91 pediatric patients with AAA at time of diagnosis. We defined three distinct pathogenetic subgroups by analyzing the frequency of hematopoietic progenitors and the frequency of activated T-cells in patients bone marrow: type I: decreased percentage of hematopoietic progenitors; type II: increased percentage of activated T-cells; type III: increased percentage of pluripotent progenitors. In 51% of the AAA patients we found a relative decreased frequency of hematopoietic progenitors and 29% of the patients demonstrated an increased percentage of activated T-cells, 25% patients showed an increased percentage of pluripotent hematopoietic progenitors. In order to characterize these distinct immunological subgroups, we investigated the plasma levels of IFN-gamma and IL15 as inhibitors and IL10 as stimulator of hematopoiesis. IL15 plasma levels were significantly elevated in AAA patients when compared to controls. In contrast we could not demonstrate a difference between IFN-gamma or IL10 plasma levels in AAA patients when compared to controls. However for IL10 and IL15 we were able to define subgroups of patients with highly elevated plasma levels of the cytokines. These data indicate that the immunopathogenesis of AAA can be heterogeneous. This heterogeneity might reflect exposure to different exogenous agents or heterogeneity in intrinsic susceptibility. The clinical impact of our findings needs to be assessed in long-term follow up of the patients.