Myasthenia gravis (MG) associated with anti-muscle-specific tyrosine kinase (MuSK) antibodies differs in many aspects from typical presentation of acetylcholine receptor (AChR)-positive MG. Myopathy and muscle atrophy are observed in MuSK-positive MG patients, unlike AChR-positive patients with MG. That is why the aim of this study was to assess the presence of myopathy and muscle atrophy as well as the tongue lipid composition in our cohort of MuSK-positive MG patients. Clinical examination, electromyography (EMG) and proton magnetic resonance spectroscopy were performed in 31 MuSK-positive and 28 AChR-positive MG patients. Myopathic EMG was more frequent in MuSK compared to AChR MG patients. In AChR MG patients, myopathic EMG in facial muscles was more frequent after long-term corticosteroid treatment, which was not the case with MuSK-positive MG patients. Facial and/or tongue muscle atrophy was registered in 23 % of MuSK MG patients. Longer disease duration was observed in patients with clinical signs of tongue and/or facial muscle atrophy compared to those with normal tongue muscle. Intramyocellular lipid deposition in the tongue was present in 85.2 % of MuSK and 20 % of AChR MG patients. Female MuSK MG patients had more frequently electrophysiological signs of myopathy on the facial muscles and signs of intramyocellular lipid deposition in the tongue, compared to male patients with MuSK-positive MG. Myopathy, muscle atrophy and intramyocellular lipid deposition in the tongue are more frequent in MuSK-positive compared to AChR-positive MG patients.