Althought it is a valuable tool for the identification of HLA alleles, sequence‐based typing (SBT) presents difficulties when used to determine HLA‐DQA1 and ‐DQB1 alleles. Specifically, some HLA‐DQA1 alleles have a three‐base deletion at codon 56 of exon 2 that interferes with the sequencing read. Moreover, the frequently used primers for HLA‐DQB1 may co‐amplify the HLA‐DQB2 pseudogene. To overcome these problems, we amplified DQA1 exon 2 using five group‐specific polymerase chain reactions (PCRs) which allowed separation of deleted from non‐deleted DQA1 alleles. DQB1 exon 2 was amplified using two group‐specific amplifications. To increase typing resolution, we also analyzed DQA1 exons 1, 3 and 4 and DQB1 exon 3 by PCR using sequence‐specific primers (PCR‐SSP) or SBT analysis. Using this method we found some important associations between DQA1 and DQB1 alleles: DQA1*05011 and DQB1*0201, DQA1*0505 and DQB1*03011, DQA1*01021 and DQB1*06, DQA1*01022 and DQB1*0502.