We have sought associations with the muscle acetylcholine receptor alpha-subunit gene (CHRNA1) in autoimmune myasthenia gravis (MG) patients from three ethnic groups; Caucasians and South Africans of Black and Mixed-Ancestry. We found a significant association with the HB*15 CA repeat allele in unrelated Black myasthenics (n = 18; RR = 2.85; pX2 = 0.04) compared with 52 ethnically matched controls. A family-based association study and linkage analysis in Caucasian simplex and multiplex families supported a positive association at this locus with the longer alleles, including HB*14 to *18. However, no significant cosegregation of the disease with the HB alleles could be demonstrated in affected sib pairs. Our results suggest that the CHRNA1 locus harbours a minor susceptibility gene for developing MG, though we cannot rule out linkage disequilibrium with another major gene locus on chromosome 2.