Hemolytic disease of newborns (HDN) and the intrauterine growth restriction of fetus (IURG) are two common perinatal disorders in the world and in Russia. In spite of many studies devoted to the pathogenesis of IUGR, its causes are not clear. One of the studied phenomena in this field is a fetal microchimerism. During the examination of the microchimerism of Human Leukocyte Antigens (HLA) genes in newborns with perinatal disorders and their mothers we performed the analysis of genes and haplotypes distribution in studied groups. The purpose of this study was to evaluate possible interactions between the inheritance of HLA genes and HDN or IUGR. The current study included 45 newborns: 23 with HDN and 22 with IUGR. The control group (108 people) consisted of 45 mothers of the examined children and the pairs (mother and her child) without perinatal disorders. The typing of 5 HLA genes was performed by the PCR-SSP method. We found that the frequency of HLA-A*25 and A*32 was significantly higher in children with HDN than in the control group. In IUGR patients HLA-C*04 was two-times more and HLA-A*02 two-times less frequent than in the healthy group. The analysis of haplotypes discovered the haplotypes which were not presented in our control. Due to the limited amount of examined patients the discovered associations between HLA genes or haplotypes and perinatal disorders need to be proved in a larger cohort of patients.