The inflammatory disease human T cell lymphotropic virus type I (HTLV-I)-associated myelopathy (HAM/TSP) occurs in only 1–2% of HTLV-I-infected individuals and is associated with a high provirus load of HTLV-I. We hypothesize that a person’s risk of developing HAM/TSP depends upon the efficiency of their immune response to the virus, which differs between individuals because of polymorphism in genes that influence this response. Previously we showed that the possession of HLA-A* 02 was associated with a lower risk of HAM/TSP, and with a lower provirus load in healthy carriers of HTLV-I. However, HLA-A* 02 did not account for all the observed difference in the risk of HAM/TSP. Here we present evidence, in the same study population in Japan, that HLA-Cw* 08 was also associated with disease protection (probability value, two-tailed test= 0.002) and with a lower proviral load in healthy carriers. Possession of the A* 02 and/or Cw* 08 genes prevented 36% of potential HAM/TSP cases. In contrast, HLA-B* 5401 was associated with a higher susceptibility to HAM/TSP (probability value, two-tailed test= 0.0003) and with a higher provirus load in HAM/TSP patients. At a given provirus load, B* 5401 appeared to increase the risk of disease. The fraction of HAM/TSP cases attributable to B* 5401 was 17%. Furthermore, individuals who were heterozygous at all three HLA class I loci have a lower HTLV-I provirus load than those who were homozygous at one or more loci. These results are consistent with the proposal that a strong class I-restricted CTL response to HTLV-I reduces the proviral load and hence the risk of disease.