We studied the expression of natural killer receptors (NKRs) on peripheral blood cytotoxic T lymphocytes and NK cells in patients who underwent an allogeneic stem cell transplant (SCT), and compared these findings with results from healthy individuals (CTRL) and patients undergoing chemotherapy (CHEMO), respectively. Peripheral blood mononuclear cells were analyzed by flow cytometry with antibodies against the NKRs CD158a, CD158b, CD158e (known as killer immunoglobulin-like receptors, KIRs), and CD94. Expression of NKRs was evaluated separately in CD56+, CD57+, and CD56/CD57 (double +) subsets of T and NK cells. We found mainly differences in CD158a and CD94 expression between the three cohorts, with the SCT and CHEMO groups usually showing similar changes, when compared to the CTRL population. None of the patients with SCT or CHEMO demonstrated patterns of restricted NKR expression. Our results provide a comprehensive overview of KIR and CD94 expression in T and NK cells following SCT and chemotherapy.