Introduction: We aimed to demonstrate the importance of serum calcitonin (Ct) and carcinoembryonic-antigen (CEA) levels in the selection of appropriate positron emission tomography/computed tomography (PET/CT) modality in the follow-up of operated patients with medullary thyroid cancer. Methods: Fourteen operated patients (8 Female, 6 Male) with MTC underwent PET/CT imaging with somatostatin (68 Ga-DOTATATE) and glucose (18 FDG) analogs due to elevated Ct or CEA at follow-up. Ct and CEA levels and both PET/CT findings were compared based on both patients and lesions. Results: Positive findings were found in 10 patients with 68 Ga-DOTATATE-PET/ CT and in 8 patients with 18 FDG-PET/CT, and sensitivity was found as 71.4% and 57.1% for both imaging methods, respectively (P > 0.05). Lesion could be detected with 68 Ga-DOTATATE-PET/CT in 3 patients in whom lesion could not be detected with 18 FDG-PET/CT. In one patient, whereas no pathological lesion was with 68 Ga-DOTATATE-PET/CT, lesion could be detected with 18 FDG-PET/CT in this patient. Of the total 67 lesions, 62 could be shown with 68 Ga-DOTATATE-PET/CT, while 48 lesions could be detected with 18 FDG-PET/CT (P < 0.05). A statistically significant positive correlation was found between Ct level and the number of lesions detected on the 68 Ga-DOTATATE-PET/CT, and similarly between CEA level and the number of lesions detected on the 18 FDG-PET/CT. Conclusions: It was found that 68 Ga-DOTATATE-PET/CT is superior over 18 FDG-PET/CT method in detection of recurrent disease in the follow-up of MTC, and serum Ct and CEA levels are important biomarkers in the selection of appropriate PET/CT modality.