The introduction of PCR-based HLA typing techniques has uncovered that the HLA system is much more variable than it has been expected from the conventional typing methods. More and more new alleles are detected which are not characterized by new sequence motifs, but by new combinations of already existing sequence motifs. This variability, reflecting the immunological necessity to have the greatest capacity for presenting antigenic peptides, is increasingly complicating DNA typing techniques based on the diversity of the coding region. We have determined the sequence of the 1st through 3rd intron of the majority of HLA-A and HLA-B alleles in 48 well-defined cell lines and 195 PCR-typed clinical samples. The few published sequences emerged to contain substantial errors. The introns turned out to be highly polymorphic. Besides extensive homologies, numerous locus- and group-specific sites could be identified. The most intriguing finding was that most of the polymorphic motifs were related to serological families. These sequence motifs were extremely beneficial for setting up PCR-based typing systems. In particular, sequencing-based typing strategies benefited from intron-restricted priming for amplification and sequencing by enabling complete analysis of the polymorphic exons. The determination of cis/trans linkages of sequence motifs was substantially facilitated. Apart from these advantages, the intron sequences were useful for evolutionary studies, delivering more insights into the genetic relationship between different alleles and the mechanisms involved in the development of the diversity of HLA. Moreover, the variability of the introns may provide a structural basis for the identification of regulatory elements acting on the level of transcription.