Despite matching of haematopoietic stem cell transplant (HSCT) patient and donor pairs across classical HLA genes HLA-A, -B, -C, -DRB1, -DPB1 and -DQB1, post-transplant complications such as graft-versus-host disease and graft failure are persistent and impact disease-free and overall survival. Haplotype matching is a potential supplement to HLA allele matching which aims at identification of SNP markers within the extended major histocompatibility (MHC) region that can be used to confer matching across other genes within the MHC region. Non-classical HLA genes have previously been described in association with clinical outcomes of HSCT and demonstrate linkage disequilibrium with classical HLA genes. This study illustrates the development of a full-gene multiplex non-classical HLA genotyping assay targeting HLA-E, -F, -G and -H, MICA and MICB. Several locus-specific primer pairs were designed for each target gene and were optimised individually to assess non-specific or off-target amplification. Selected primer pairs were multiplexed based on amplicon size and sequenced using Oxford Nanopore MinION sequencing. Across 48 IHW samples sequenced, a total of 238 alleles were identified to a minimum of three fields of typing resolution. While complete exon sequences were obtained for all alleles, the presence of large homopolymers within intronic regions of some loci prevented full-length allele sequences from being obtained. Previous results were available for 134/238 alleles, 130 of which were concordant, and 4 discrepant with results in the IMGT-IPD database, prompting further investigation. Numerous novel polymorphisms and extended sequences were characterised in this study to be submitted to the IPD-IMGT database for curation. While little association analysis can be performed based on the small sample size, this study prompts larger-scale population analysis to elucidate associations between the classical and non-classical genes, and markers within extended MHC haplotypes. This information can then be used to investigate the clinical benefit of haplotype matching in HSCT.