The HLA complex plays a prominent role in predisposition to many autoimmune diseases. Thus far, the highly polymorphic class I and class II loci have been considered as the prime candidates to explain this role. There is nonetheless growing evidence that other closely linked HLA loci are also involved in autoimmune susceptibility. Their search, however, has been hampered by the often strong linkage disequilibria, i.e. the non-random association of alleles at linked loci, across the HLA complex. Here, we discuss recent work from our laboratory on the dissection of this emblematic genetic region in a model autoimmune disease, acquired myasthenia gravis (MG).