The use of direct sequencing as a typing strategy is well acknowledged. Direct sequencing identifies all sequence motifs including new polymorphisms in heterozygous sequences. The earlier protocols for human leukocyte antigen HLA-DQB1 Sequencing-Based Typing (SBT) frequently encounter preferential amplification of one of the alleles that can lead to unreliable sequences or even to allelic dropout. In our new approach, the quality of the exon 2 sequences, now including both alleles to the same extend, was achieved by amplifying the HLA-DQB1*05/06 group into two groups by changing the common 3′ amplification primer. In combination with exon 3 this updated HLA-DQB1 protocol provides a reliable approach for heterozygous sequencing.