The C-type lectin-like receptor CD161 is a well-established marker for human IL17-producing T cells, which have been implicated to contribute to the development of graft-versus-host disease (GVHD) after allogeneic stem cell transplantation (allo-SCT). In this study, we analyzed CD161⁺ T cell recovery, their functional properties and association with GVHD occurrence in allo-SCT recipients. While CD161⁺CD4⁺ T cells steadily recovered, CD161^hiCD8⁺ T cell numbers declined during tapering of Cyclosporine A (CsA), which can be explained by their initial growth advantage over CD161^neg/lowCD8⁺ T cells due to ABCB1-mediated CsA efflux. Interestingly, occurrence of acute and chronic GVHD was significantly correlated with decreased levels of circulating CD161⁺CD4⁺ as well as CD161^hiCD8⁺ T cells. In addition, these subsets from transplanted patients secreted high levels of IFNγ and IL17. Moreover, we found that CCR6 co-expression by CD161⁺ T cells mediated specific migration towards CCL20, which was expressed in GVHD biopsies. Finally, we demonstrated that CCR6⁺ T cells indeed were present in these CCL20⁺ GVHD-affected tissues. In conclusion, we showed that functional CD161⁺CCR6⁺ co-expressing T cells disappear from the circulation and home to GVHD-affected tissue sites. These findings support the hypothesis that CCR6⁺CD161-expressing T cells may be involved in the immune pathology of GVHD following their CCL20-dependent recruitment into affected tissues.