We describe and functionally characterize six mutations of the acetylcholine receptor (AChR) ε subunit gene in three congenital myasthenic syndrome patients. Endplate studies demonstrated severe endplate AChR deficiency, dispersed endplate regions and well preserved junctional folds in all three patients. Electro-physiologic studies were consistent with expression of the fetal γ-AChR at the endplates in one patient, prolongation of some channel events in another and γ-AChR expression as well as some shorter than normal channel events in still another. Genetic analysis revealed two recessive and heteroallelic e subunit gene mutations in each patient. One mutation in each (εC190T [εR64X], ε127ins5 and ε553del7) generates a nonsense codon that predicts truncation of the ε subunit in its N-terminal, extracellular domain; and one mutation in each generates a missense codon (εR147L, εP245L and εR311W). None of the mutations was detected in 100 controls. Expression studies in HEK cells indicate that the three nonsense mutations are null mutations and that surface expression of AChRs harboring the missense mutations is significantly reduced. Kinetic analysis of AChRs harboring the missense mutations show that εR147L is kinetically benign, εP245L prolongs burst open duration 2-fold by slowing the rate of channel closing and εR311W shortens burst duration 2-fold by slowing the rate of channel opening and speeding the rate of ACh dissociation. The modest changes in activation kinetics are probably overshadowed by reduced expression of the missense mutations. The consequences of the endplate AChR deficiency are mitigated by persistent expression of γ-AChR, changes in the release of transmitter quanta and appearance of multiple endplate regions on the muscle fiber.