Background: The encapsulated follicular variant (EFV) of papillary thyroid carcinoma (PTC) is the most discussed entity in thyroid pathology. Recently, the question of whether or not EFV-PTC is a malignant entity has been the subject of renewed discussion in the light of recent molecular and clinical studies. The aim of this study was to analyze the malignancy ratios of each category of the Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) if EFV-PTC is no longer considered as a malignant entity. Materials and Methods: Data on thyroid fine-needle aspirations (n = 1,886) with surgical follow-up between 1999 and 2014 were studied. EFV-PTC cases constituted 27% (94/343) of the malignant cases. Results: Malignancy ratios were determined as nondiagnostic, benign, atypia/follicular lesion of undetermined significance, suspicious for follicular neoplasm/follicular neoplasm, suspicious for malignancy, and malignant categories of the TBSRTC in 13, 7, 45, 30, 72 and 98%, respectively. If EFV-PTC was not regarded as malignant, malignancy ratios would decrease to 6.5, 6, 30, 10, 48, and 87% for each category in the same order. Conclusions: The current study showed that the most significant decrease in relative malignancy ratios was seen in the suspicious for follicular neoplasm/follicular neoplasm category (66% relative decrease), but all categories represented a considerable decrease.