Most cases of hemolytic disease of the newborn associated with anti-Jra are mild. However, rare cases of hydrops fetalis and severe anemia have been reported. We treated a neonate with anemia who was born with maternal anti-Jra, which were detected in the umbilical cord plasma. The Jra antigens in the neonate core blood red blood cells (RBCs) exhibited extremely weak reactivity to PEG-IAT, an anti-Jra reagent. However, upon re-examination of Jra antigen using PEG-IAT at 3 months postpartum, positivity was observed. Thereafter, upon performing PCR-SSP analysis of blood relatives targeting ABCG2 at positions 376 and 421, we found that the mother was Jr(a-) with 376 T homozygosity, whereas the father was Jr(a+) with 376 C homozygosity and a carrier of a 421 C > A mutation. The first sibling, like the propositus, was Jr(a+), exhibiting 376 CT heterozygosity. However, the first sibling carried a 421 C > A mutation, whereas the propositus had no mutation at position 421. Setting the normal Jra (a+) type (376 C, 421 C) to 100 %, we identified the amount of Jra in RBC using FCM to be 82 % in the father, 31 % in the first sibling, and 69 % in the propositus. Furthermore, upon comparing peripheral blood and myelograms of the neonate at the time of birth, we found a low myeloid cells/erythroid cells ratio, undifferentiated erythroblasts, and reduced megakaryocytes. On the basis of these findings, we suggest that cell surface antigen is involved in the HDN caused by anti-Jra, and that a cytodifferentiation abnormality is present in the hematopoietic system.