Objective To determine the capability of serum amyloid A (SAA) in differentiating attacks of familial Mediterranean fever (FMF) from acute febrile upper respiratory tract infections. Method Children diagnosed with FMF during febrile attacks were recorded as the patient group. The control group consisted of children with febrile upper respiratory tract infections. Complete blood count, serum amyloid A (SAA), C-reactive protein (CRP), and erythrocyte sedimentation rate were recorded in both groups during febrile episodes. Results The cohort consisted of 28 children with FMF attack and 28 previously healthy children with acute febrile infection. While CRP and SAA levels were elevated in both groups, elevations during FMF attacks were significantly higher in the FMF group than in the control group. Median CRP was 85 mg/L in the FMF attack group and was 36 mg/L in the control group (p = 0.001). Median SAA was 497.5 mg/L in the FMF attack group and was 131.5 mg/L in the control group (p < 0.001). Correlation analyses showed that SAA and CRP were positively correlated in the FMF attack group (r = 0.446, p = 0.01). The best cut-off value for SAA in differentiating FMF attack from an acute febrile infection was 111.5 mg/L (sensitivity 100%, specificity 65.1%, area under curve (AUC) = 0.78, confidence interval 0.66-0.90, p < 0.001). Conclusion Serum amyloid A is a sensitive but not specific marker for demonstrating inflammation in FMF. SAA levels rise substantially in febrile upper respiratory tract infections.