A1 serotype positivity is roughly linked to a large number of inflammatory diseases and conditions believed to have immune system involvement.

While it is not clear what role A1 has in infectious disease, some linkage with infection rates in HIV remain associated within the A1 region of the haplotype.

In all instances so far, HLA-A1 has been found to be linked to disease by association, but there are few that define HLA-A1 has a predominant genetic risk relative to other gene-alleles in the vicinity of the A1 gene on the larger haplotype.

[4] A recent study of DR3-DQ2/DR4-DQ8 phenotype found that A1-cw7-B8 was actually lower than expected relative to other A-B types, indicating that risk associated genes are located between B8 and DR3.

[5] The type 1 diabetes example shows the inherent difficulty in the use of linkage analysis alone to cipher risk.

[10][11][12] Some diseases found associated with A1 actually link to the extended A1-B8 haplotype, viral induced hepatitis and accelerated progression of HIV are examples.

For example, A*01:02 was found linked to a type of stroke seen frequently in children with sickle cell anemia.