The study was designed to evaluate the molecular and serological features of a newborn with severe hemolytic disease of the newborn (HDN) caused by anti-Jk3, and to further rich our understanding of Kidd subgroup genetics using pedigree analysis which is the first analysis of a Jk null phenotype in China and the first report of severe HDN caused by anti-Jk3. A female baby presented with hyperbilirubinemia (36 μmol/L) on the day of birth. Antibody screening tests using blood samples from the patient and her family indicated that the mother’s plasma contained alloantibodies against high frequency antigens and the results of direct Coombs test were all negative. Kidd phenotypes were Jk(a-b-), Jk(a-b+), and Jk(a-b+) in the mother, father, and baby, respectively. Kidd genotype was determined by PCR amplification of a single nucleotide polymorphism (838) and all family members were Jk(a-b+). Kidd gene exons 4 to 11 were sequenced to identify potential mutations.Sequencing analysis revealed that c.838 G>A and intron c.3 -78 G>A homozygosity occurred in all family members along with homozygosity and heterozygosity for c.IVS5-1G>A in the mother and newborn, respectively. In conclusion, serological and genetic analyses confirmed that the Jk(a-b-) phenotype was caused by homozygous IVS5-1G>A mutation of the Kidd gene. This result is consistent with that of a previous report and presents a useful diagnostic tool to identify HDN caused by anti-Jk3. A further study is required to identify the effect of intron 3 -78 G>A mutation on phenotype.