Background Familial Mediterranean Fever (FMF) is a periodic auto-inflammatory disease with multiple systemic manifestations. This study aims to describe the various musculoskeletal and neurological manifestations in a cohort of Egyptian FMF patients and to evaluate their relation to the different Mediterranean fever gene (MEFV) mutations. Results This study involved 145 FMF patients, of them 62.1% were females and 31.7% were of the pediatric age. All involved patients had homozygous MEFV gene mutation. The presenting manifestation in 71.9% of these patients was abdominal pain followed by musculoskeletal manifestations in 35.2% of them. 38.6 % of the involved patients had arthritis during the period of follow-up. Monoarthritis was the most frequent pattern of arthritis. Arthralgia was present in 96.6% of the studied patients. Myalgia was present in 19.3% of the studied patients especially involving the lower limb muscles with one case of protracted febrile myalgia. Neurological manifestations were present in about 86.9 % of patients with vertigo, paresthesia, and seizures as the most common. Five major MEFV gene mutations were found in most of the studied patients (135 patients): M694V, M680I, E148Q, V726A, and M694I. When a comparative study was done between these five major mutations according to the age of onset of the symptoms, different musculoskeletal and neurological manifestations, ESR, serum amyloid level and dose of colchicine, no statistical difference was found. Conclusion Musculoskeletal manifestation is the second most common presenting symptom in a cohort of Egyptian FMF patients after abdominal pain. Arthralgia is the most frequent musculoskeletal manifestation while monoarthritis of the knee or ankle joint is the most common pattern of arthritis in FMF patients. Vertigo, paresthesia, and seizures are the most frequent neurological manifestations. Musculoskeletal manifestations, neurological manifestations, serum amyloid level, and dose of colchicine are not related to the type of the genetic mutation in this cohort.