RhD negative individuals are rare and only account for 0.3-0.5% of Taiwanese population. There are some variations among Chinese RhD negative individuals and the molecular basis of these variants is unknown. Two hundred and four RhD negative DNA samples were investigated by a modified polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) and RT-PCR. Several representative cases were further studied using Southern blot analysis. Three types of genetic change in RhD negative individuals were discovered in the Taiwanese population. The most common one, accounting for 150 (73.5%) of 204 cases, was a deletion of the D gene with expression of normal ce or cE antigens (72.5% ce, and 1.0% cE), which were produced by the ce or cE allele of the RHCE gene. The second one, Del, was a deletion of 1013 bp between introns 8 and 9 including exon 9 of the RHD gene. This type accounted for 41 (20.1%) of 204 D negative individuals. The third type was caused by genomic rearrangement around intron 2 and intron 9 between the RHD and RHCE genes and it results in a hybrid gene (D-CE-D) with exons 1, 2 and 10 belonging to the RHD gene. This type of recombination accounted for 13 (6.4%) of 204 D negative individuals. The RhD negative variants found in this study are combination of two of the three alleles, described above. The PCR methods, which detect the differences in introns 1, 2 and 4 or exon 7 for differentiating D positive and D negative, are not reliable methods for studies in the Chinese population.