The prognosis of differentiated thyroid cancers (DTC) read at cytology as indeterminate and classified as Thy 3 according to the British Thyroid Association has recently been suggested to be good. To obtain robust information about this potential novelty, in this study we retrospectively reviewed DTC with a prior fine-needle aspiration cytology (FNAC) of Thy 3, Thy 4 or Thy 5 presently followed up at two institutes. Patients with no FNAC before surgery were excluded and a series of 284 DTC was enrolled in the study. Of these, 53 had Thy 3, 108 Thy 4, and 123 had Thy 5 prior to surgery. At histology, 280 (98.6 %) papillary and 4 follicular (1.4 %) cancers were found. Overall, the less aggressive cancer forms were prevalent in all three groups. The lower TNM stages (I and II) were more frequent in the Thy 3 group (96.2 %) than in the other cases (76.6 %) (p < 0.001). Neck lymph node metastasis at diagnosis was found in 3.8 % of Thy 3, 18.5 % of Thy 4, and 26 % of Thy 5 cases. At follow-up, a 16.2 % recurrence rate was recorded, ranging from 1.9 % in Thy 3 group to 19.5 % for Thy 4 and Thy 5 (p < 0.001). According to the Kaplan-Meier curve, Thy 3 was thus a favorable prognostic factor compared with Thy 4 and Thy 5 (OR = 0.079, p < 0.001, 95 %CI 0.01-0.59). At multivariate analysis, Thy 3 was an independent predictor of good prognosis (OR = 0.06, p = 0.03, 95 %CI 0.01-0.80). In conclusion, DTC with a preoperative Thy 3 cytology have a better prognosis than those with Thy 4 and Thy 5 due to less aggressive tumor types and lower TNM stage at diagnosis.