Background: Juvenile-onset systemic lupus erythematosus ((j)SLE) is an autoimmune/inflammatory disease that can result in significant damage and disability. Familial Mediterranean Fever (FMF), the most common periodic fever syndrome in children, is characterized by episodes of fever, abdominal pain, arthralgia, arthritis, serositis. Given the overlap in clinical features between jSLE and FMF, we sought to assess the prevalence of the common 12 MEFV gene mutations in a group of jSLE patients. Methods: This cross-sectional controlled study analyzed MEFV gene mutations in 60 jSLE patients and 30 healthy controls using PCR and reverse hybridization. The assay included the following gene mutations E148Q, P369S, F479L, M680I (G/C), M680I (G/A), I692del, M694V, M694I, K695R, V726A, A744S, and R761H. Results: Heterozygous MEFV gene mutations were found in 10% of jSLE patients and 13% of the controls, with no statistically significant difference. These mutations were primarily located in exon 10. Fever, abdominal pain, arthritis, and pericardial effusion were the most common clinical presentations in jSLE patients with a heterozygous MEFV gene mutation. Conclusions: jSLE patients carry MEFV variants at rates comparable to the general population. Nevertheless, MEFV genetic mutations may influence the presentation of SLE. Clinicians should consider the possibility of co-occurrence of both diseases in patients with overlapping symptoms. Wider scale studies are needed to validate our findings