The aim of this study was to evaluate the risk of malignancy (RoM) in category III thyroid nodules of the Bethesda system in patients with and without Hashimoto thyroiditis (HT) and to analyze whether obtaining category III with a repeat FNA (rFNA) increases RoM. The study included 563 HT and 1250 non-HT patients; rFNA was performed in 349 and 575 patients, and surgical treatment in 160 and 390, respectively. There was no difference in RoM between HT and non-HT patients in the whole examined population (lower limit of RoM), nor in operated patients (upper limit of RoM), HT: 5.0–17.5%, non-HT: 4.7–15.1%. RoM in patients with AUS nodules (with nuclear atypia) was similar in both groups (HT: 21.7–40.0%, non-HT: 16.9–41.4%), as it was in patients with FLUS nodules (with architectural atypia) (HT: 3.5–13.3%, non-HT: 4.0–13.0%). In patients from both groups together, with category III diagnosed twice and AUS identified at least once, RoM was 16.7–50.0% and it was higher than that in patients with FLUS nodule diagnosed twice: 3.2–13.0% (p < 0.005). Concluding, RoM in category III nodules is not affected by the presence of HT. Subcategorization of category III nodules (FLUS vs. AUS) may provide guidance toward further follow-up or surgery in both groups.