Chronic myelogenous leukemia (CML) results from a translocation (9;22), which creates an immunogenically active BCR-ABL fusion protein. Previous authors have reported both positive and negative human leukocyte antigen (HLA) associations with CML, possibly as the result of different antigenic peptide presentation capabilities. We examined HLA Class I and Class II antigen polymorphisms in 31 patients with CML and compared these with 258 control individuals drawn from Maritime Canada. HLA-B*13 (odds ratios (OR) 4.92, 95% confidence intervals (CI) 1.70-14.24), HLA-B*55 (OR 4.50, 95%CI 1.07-18.99), and HLA-DRB1*16 (OR 4.07, 95%CI 1.17-14.09) were all statistically significant risk markers for CML. After a Bonferroni correction for Type I error was applied, only HLA-B*13 remained statistically significant as a risk marker for CML. No HLA antigens were found to be protective. The lack of reproducibility of HLA antigen associations with CML suggests that these associations are population-specific and may not be due to HLA antigen-restricted differences in CML antigen presentation.