Recent studies suggest that exposure of the fetus and newborn to non-inherited maternal major histocompatibility complex HLA antigens (NIMA) has a life-long effect on allograft recognition that could influence tolerance of organ grafts. NIMA also appear to influence disease susceptibility. Here, Jon van Rood and Frans Claas discuss evidence that three HLA haplotypes, those inherited from the parents plus NIMA, shape the immune response.