The disorders of the neuromuscular junction seen in children, the congenital myasthenic syndromes and autoimmune myasthenia gravis, are very rare. Their clinical symptoms and signs may be variable, most notably in the neonate and infant. They should enter the differential diagnosis of many different clinical presentations, such as 'floppy infant' or attacks of episodic apnoea. Many molecular genetic abnormalities have been discovered in congenital myasthenic syndromes, but screening for these is impracticable without confirmation of a disorder of the neuromuscular junction. In this review, the different neurophysiological tests that can be used are discussed, with their merits and contraindications in children. After consideration of the acceptability of the different techniques, it has been found that stimulation single-fibre electromyography (stimSFEMG) of orbicularis oculi seems to be the best choice in children. In most instances it can be performed on the conscious child and it has a good specificity and high sensitivity. A protocol for using stimSFEMG is described.