One hundred and fifty‐eight Kadazan, Iban and Bidayuh individuals registered with the Malaysian Marrow Donor Registry were typed for human leukocyte antigen (HLA)‐A, HLA‐B and HLA‐DR. Six, seven and eight HLA‐A alleles as well as 13, 15 and 16 HLA‐B alleles were detected in the Kadazan, Bidayuh and Iban, respectively. The most common HLA‐A allele in all three groups was HLA‐A*24 with a frequency of 0.456, 0.490 and 0.422 in the Kadazan, Bidayuh and Iban, respectively. The most common HLA‐B allele detected in the Kadazan was HLA‐B*40 with a frequency of 0.333; for the Bidayuh and the Iban it was HLA‐B*15 with a frequency of 0.460 and 0.275, respectively. The HLA‐DR allele with the highest frequency in the Kadazan was HLA‐DR*1502 with a frequency of 0.500. In the Iban and the Bidayuh, HLA‐DRB1*1202 was the most common DR allele with frequencies of 0.235 and 0.310, respectively. The two most common haplotypes for the Kadazan are A*34‐B*38‐DR*1502 and A*24‐B*40‐DR*0405, whereas for the Bidayuh they are A*24‐B*15‐DR*1602 and A*24‐B*35‐DR*1202 and for the Iban they are A*34‐*B15‐DR*1502 and A*24‐B*15‐DR*1202.