Background: In Myasthenia gravis (MG), autoantibodies target neuromuscular junctions (NMJ) proteins leading to a decreased sensitivity to ACh with muscle weakness. 80- 88% of MG patients have AChR antibodies (AChR-Ab+ve). It was suggested that AChR-Ab-ve patients may have autoantibodies against other NMJ proteins or a more sensitive assay is required to detect AChR-Abs. Hoech, etal (2001) detected Muscle specific kinase antibodies (MuSK-Abs) in 70% of AChR-Ab-ve generalized MG patients (GMG). Leite, etal (2008) detected clustered AChR-Abs by the cell based assay (CBA) in 66% of AChR-Ab-ve patients. A considerable proportion of MG patients remain seronegative for NMJ autoantibodies (SN-MG). Objectives:To identify the nature of NMJ autoantibodies in AChR-Ab-ve MG patients from Sudan and to relate it to their clinical presentationPatients and Methods: 96 MG patients (77 GMG and 19 OMG) were randomly recruited from two national MG referral centers in Khartoum during the period 2010- 2012. All patients were screened for AChR-Abs and MuSK-Abs by radioimmunoprecipitation assay (RIPA). Negative sera were screened for clustered AChR-Abs by the CBA.Results: 62.5% (60/96) of patients were AChR-Ab+ve by RIPA. Of the 36 AChR-Ab-ve patients, 19.4% (7/36) were MuSK-Ab+ve, and 22.2% (8/36) were Clustered AChR-Ab+ve. 21.9% (21/96) of patients remained SN-MG. MuSK-Ab+ve patients (MuSK-MG) represented 25.9% (7/27) of AChR-Ab-ve GMG with a female: male ratio of 1.3:1 and dominant bulbar symptoms (85.7%, 6/7). Clustered AChR-Ab+ve patients were all females (n=8). SN-GMG were predominantly females (92.9%, 13/14) (P=0.02). The incidence of an associated autoimmune thyroid gland disease (AUID) in SN-GMG females was 53.8% (7/13) compared to 17.6% (6/34) in AChR-Ab+ve GMG females (P<.013), RR (95% CI)=3.05 (1.3-7.38).Conclusion: In MG patients with ACHR-Ab -ve by the RIPA, only 58.3% were found to be truly seronegative to known MG antibodies, 19.4% were MuSK MG and 22% were positive to clustered AChR-Ab. The association between AUID and SN-GMG females suggests the involvement of sex and predisposition to autoimmune thyroid gland diseases in the pathogenesis of SN-MG