© 2020, Author(s).Objectives: The aim of this study was to evaluate the effect of amyloid deposition in colon mucosa on the results of anorectal manometry test and the use of ROME III questionnaire in patients with Familial Mediterranean Fever (FMF). Methods: The files of patients diagnosed with FMF were scanned to evaluate the patients at risk for amyloid deposition. Predisposing factors were identified. The patients were sampled using anorectal manometry test, Rome III questionnaire and the rectal mucosa suction biopsy and the test results were compared. Results: 17 (63%) of the patients were female and 10 (37%) were male. The mean age was 12.15 ± 2.40 years. The number of patients with amyloid deposition in the rectal mucosa sample was 2 (7.4%). Both of these patients had regularly used colchicine. Amyloid deposition was found to be high in patients with M694V homozygous mutation (P = 0.05). According to the Rome III questionnaire, findings suggestive of irritable bowel syndrome were found in 5 patients and abdominal migraine was found in 3 patients. However, no statistical difference was found when the results of the Rome III questionnaire were compared with the results obtained from the anorectal manometry test (P > 0.05). Conclusions: Amyloidosis can be seen due to various environmental factors, regardless of age, even when colchicine is regularly used. Anorectal manometry is an easy to perform test, helping diagnosis in this patient group. Although it has been shown that in patients with predisposing factors for amyloid deposition RAIR can be detected at lower pressures in anorectal manometry, the clinical significance of this finding is unclear. Since the Rome III questionnaire showed findings consistent with functional abdominal pain disease in one third of the patients, independent of the presence of FMF, it was found that the application of this questionnaire in patients with FMF could be misleading.