BACKGROUND: Minor histocompatibility antigens have been poorly defined. Whether Duffy (FY) and Kidd (JK), polymorphic and immunogenic blood group antigens, widely distributed in human organs, expressed and functional in the kidney, could function as minor histocompatibility antigens and be implicated in renal allograft rejection was questioned. STUDY DESIGN AND METHODS: A retrospective, homogeneous, single-center cohort of 370 renal transplants was analyzed. In all donor/recipient pairs, FY and JK polymorphisms were identified by real-time polymerase chain reaction. In all donor/recipient pairs the matching (m) or mismatching (mm) status was defined for both systems. All biopsies were reviewed, and historical screening results for FY and JK alloantibodies and graft survival were retrospectively analyzed. RESULTS: Although graft survival was not different between the groups, it was observed that FY mm grafts had significantly more chronic lesions compared to FY m grafts. HLA-DR11 was more frequent in both recipients (p = 0.0081) and donors (p = 0.0104) of FY mm couples without chronic allograft nephropathy, suggesting a protective effect for this molecule. JK mm grafts had more interstitial inflammation than JK m grafts (p = 0.0369). CONCLUSION: This renal model unmasks for the first time the role of FY and-to a lesser extent-JK antigens as minor histocompatibility antigens and suggests their potential role for other clinical transplant settings.