Prevalence of autoantibodies targeting the neuromuscular junction in autoimmune myasthenia gravis (MG ) varies among different populations, probably due to genetic and environmental differences. We present a cross sectional, case-control study carried in the years 2011- 2012. The study aimed to detect the prevalence of AChR-Abs, and MuSK-Abs in Sudanese MG patients, and to relate the autoantibodies status to their clinical presentation. The study was ethically approved. 59 MG cases were recruited from two national MG centers in Khartoum and matched by age and sex to 157 controls. AChR-Abs and MuSK-Abs were measured in plasma, using radioimmunoprecipitation assay (RIPA) (1).Plasma from patients who tested negative for both autoantibodies by the RIPA were further tested for low affinity AChR-Abs by the Cell Based Assay (CBA) (2). AChR-Abs were detected in; 76.3% of all MG patients (median, IQR= 1.6, 0.2- 26 nmol/L), 80 % of generalized MG patients (GMG), 64 % of ocular MG patients, and 3.8% of the controls (median, IQR= 0.1, 0.01- 0.16 nmol/L). MuSK-Abs were detected in; 16.7% of AChR-Ab-ve GMG patients, 1/33 of AChR-Ab+ve GMG patients, and 1/106 of the controls. 20% of MG patients remained seronegative for both autoantibodies. AChR-Ab+ve GMG patients and seronegative GMG patients were not significantly different regarding disease severity. Seronegative GMG patients were all females (7/7) (P<.05, Fisher’s Exact test). The prevalence of associated autoimmune diseases (AuID) was 86 %( 6/ 7) in seronegative GMG patients and 14% (5/35) in AChR-Ab+ve GMG patients; relative risk 6 (2.5 to 14.27) (P= 0.001, Fisher’s Exact test). MuSK-Ab+ve cases were two late onset MG males (onset >40 years), one early onset MG female, and had dominant bulbar symptoms. This study provided the first insight into autoantibody profile of MG patients in an Arabian- African population. The detection rates of AChR-Abs and MuSK-Abs were within the range of detection rates in other series. Some clinical features (sex and AuID) were found to be related to the autoantibody status of MG patients. These findings suggest involvement of factors like sex and genetic susceptibility to autoimmune diseases in determining the pathogenesis and homeostasis of autoantibodies in MG.