Abstract We studied the pathophysiology of aplastic anaemia (AA) in six different pairs of relatives without a family history of hematologic disorders or congenital AA. Five and four of the six pairs shared the HLA‐DRB1*15:01 and B*40:02 alleles, respectively. Glycosylphosphatidylinositol‐anchored protein‐deficient blood cells were detected in eight of the 10 patients evaluated. In a mother‐daughter pair from one family, flow cytometry detected leukocytes lacking HLA‐A2 due to loss of heterogeneity in chromosome 6p. Whole‐exome sequencing of the family pair revealed a missense mutation in MYSM1. These results suggest that genetic inheritance of immune traits might underlie familial AA in some patients.