Our understanding of the immunological processes influencing the clinical outcome after kidney transplantation has advanced majorly over the last few decades. However, many factors still restrict graft and patient survival. Within the Maastricht transplant center we have successfully implemented an alternative immunosuppressive regimen involving Tacrolimus monotherapy in order to minimize the adverse effects associated with long-term use of immunosuppressive drugs. This clinical development has an impact on pre-transplant risk stratification which requires that patients are closely monitored immunologically. In this review we will elaborate on our strategy regarding the analysis of epitopes in HLA-DQ and HLA-DP molecules. In this respect we have also looked at the immunodominance of certain epitopes by assessing their structural localization, conformation and physiochemical properties.