Atypia and follicular lesions of undetermined significance (AUS/FLUS) is the most controversial category of The Bethesda System. The risk of malignancy (ROM) in this group is estimated as 5–15%, however, the occurrence of two or more subsequent biopsy results with AUS/FLUS diagnosis makes these clinical situations more complex. We evaluated the ROM and prognostic value of aggressive ultrasound (US) features in 342 patients with thyroid nodules (TNs) with subsequent biopsy results of AUS/FLUS. We assessed US features and compared them with the final histopathological diagnosis. Overall, 121 (35.4%) individuals after first AUS/FLUS diagnosis underwent surgery and 221 (64.6%) patients had repeated biopsies. The ROM after first, second, and third biopsies with subsequent AUS/FLUS diagnosis were 7.4%, 18.5%, and 38.4% respectively. We demonstrated significantly higher rates of occurrence of aggressive US features in patients with malignancy (p < 0.0001). The age <55 years old was also a significant risk factor for TC (p = 0.044). Significant associations were found between aggressive US features and malignancy in patients after first diagnosis of AUS/FLUS (p < 0.05). The juxtaposition of US features with the number of biopsy repetitions of TN with consecutive AUS/FLUS diagnoses may simplify the decision-making process in surgical management. Two or three consecutive biopsy results with AUS/FLUS diagnosis increases the ROM.