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Aim Genomic alterations and somatic mutations have been widely identified in hematologic malignancies. Recent studies have described mutations in different HLA genes of these patients. These mutations are identified when high resolution typing is needed for patients and potential donors. An African American patient treated for myeloma, received an autologous stem cell transplant in 2010. During 2011 he was diagnosed with a secondary plasma cell leukemia, becoming a candidate for an allogeneic stem cell transplant. Methods HR HLA typing was performed by Sequence Based Typing (SBT) methodology and a single base mismatch on one of his HLA-DQB1 allele was identified in exon 2, codon 13, leading to an amino acid substitution (Glycine to Valine). Three siblings, considered potential donors, had HLA typing performed and the same HLA-DQB1 ∗ 06:XX was identified in two of them. To investigate the HLA-DQB1 novel allele segregation and its origin within the family, their mother was typed. Results One of the HLA-DQB1 alleles identified did not match with DQB1 alleles from HLA database 3.6.0, used for the SBT data analysis. Their mother HLA typing identified HLA-DQB1∗06:02:01 and DQB1 ∗ 06:XX. The alleles DQB1 ∗ 06:XX and DQB1 ∗ 06:02:01 differ by 1 nucleotide mismatch in exon 2, which caused us to question what genetic alterations that may have occurred in her DQB1 genes. Conclusions Our findings demonstrate that the hematological malignancy is not always the cause for HLA genes alterations, which reinforces the value of family studies to explain gene segregation. Beyond the implications of obtaining an accurate HLA typing and donor selection, these genetic alterations on HLA genes may allow some mechanisms of immune surveillance to fail when associated with other complications caused by hematological malignancies affecting bone marrow transplant candidates. The allele in question was also identified by another HLA laboratory, and is included in the most recent IMGT HLA alleles update, it was named HLA-DQB1 ∗ 06:49.