The aim of this study is to characterize Treg (FOXP3) and Th17 (RORC)-related genes in patients who underwent hematopoietic cell transplantation (HCT) and correlate them with graft-versus-host disease (GVHD) onset and patients' outcome. Fifty-one patients undergoing allogeneic HCT from matched related donors (MRD) were studied. Samples were collected before HCT, at acute (aGVHD) or chronic GVHD (cGVHD) onset, and 90 days post-HCT for those who did not have signs of aGVHD. FOXP3 and RORC gene expressions were assessed by real-time PCR (qPCR) as representatives of Treg and Th17 cells, respectively. We found increased expression of proinflammatory Th-17 related RORC in cGVHD compared with patient without GVHD; also, we found decrease in Treg-related FOXP3 expression in the samples at the time of GVHD when compared to its respective samples before HCT. Although these results could have therapeutic relevance, we could not identify genes' expression values to be used to predict GVHD onset, overall survival, non-relapse or relapse-related mortality.