Complement activation at motor endplates is the primary effector mechanism in myasthenia gravis (MG). In this study, we evaluated whether differences in gene transcript levels and protein expression of cell-surface complement regulators could be a factor in the increased susceptibility of extraocular muscle (EOM) compared to other skeletal muscles to MG. Experimental autoimmune MG (EAMG) was induced in mice by administration of a monoclonal antibody (mAb) directed toward the acetylcholine receptor (AChR). Standard RT-PCR and real-time PCR (qPCR) were used to assess mRNA levels of decay-accelerating factor (DAF), CD59, and complement receptor 1-related gene/protein y (Crry). Gene transcript levels of the α- and γ-subunits of the AChR were also evaluated by qPCR. Protein expression of the three intrinsic complement regulators at the neuromuscular junction was assessed by immunohistochemistry. Under constitutive conditions by RT-PCR, no significant differences were detected, but qPCR, EOM showed lower mRNA levels of all three complement regulators, but higher levels of α- and γ-subunit gene transcripts. With EAMG, significant decreases in mRNA levels of all three complement regulators as well as AChR subunits occurred in EOM, but not in the diaphragm. Immunoreactivity for all three complement regulators was highly concentrated at diaphragm junctions, whereas it was less intense or absent at EOM junctions. With EAMG, immunoreactivity for Crry and DAF increased at diaphragm junctions and for DAF at EOM junctions. Diminished intrinsic complement regulatory activity may contribute to the susceptibility of EOM to MG. Our findings suggest that complement inhibitor-based therapies could be useful in treating ocular manifestations of MG.