Allogeneic hematopoietic stem cell transplantation (HSCT) is widely used to treat hematopoietic cell disorders, but is often complicated by graft versus host disease (GvHD) that causes severe epithelial damage. Here we have investigated longitudinally the effects of induction chemotherapy, conditioning radio-chemotherapy and allogeneic HSCT on composition, phenotype and recovery of circulating innate lymphoid cells (ILC) in 51 acute leukemia patients. We found that reconstitution of ILC1, ILC2 and NCR(-) ILC3 was slow compared to that of neutrophils and monocytes. NCR(+) ILC3 which are not present in the circulation of healthy individuals appeared both after induction chemotherapy and after allogeneic HSCT. Circulating patient ILC before transplantation as well as donor ILC after transplantation expressed activation (CD69), proliferation (Ki-67) and tissue homing markers for gut (α4β7, CCR6) and skin (CCR10 and CLA). The proportion ILC expressing these markers was associated with a decreased susceptibility to therapy-induced mucositis and acute GvHD. Taken together, these data suggest that ILC recovery and treatment-related tissue damage are interrelated and affect the development of GvHD.