This review focuses on six transcendental aspects that affect transplant immunology in Mexico: in first place, several immune factors which may lead to graft loss are highlighted; then, some features of the biological variability present in Mexican populations are pointed out in the context of their adaptive and sociopolitical history, leading to the discussion on the genetic diversity within the major histocompatibility complex (MHC) and the importance of resolution in genotypic characterization of the human leukocyte antigen (HLA) and related systems on the basis of human intra-population variability. Critical points on the interpretation of serological reactivity of anti-HLA antibodies are discussed in function of allelic frequency as a probability of finding a variant in a finite population. Finally, evidence of influence of other genetic systems on the recipient-graft relationship is emphasized.