Purpose: False negative results of fine needle aspiration biopsies (FNAB) remain one of the most important problems in the management of thyroid nodules. The aim of this study was to evaluate the factors affecting the false negative results of FNAB, especially in thyroid nodules with indeterminate cytology.
 Materials and Methods: Patients with thyroid nodules who underwent FNAB and subsequent thyroidectomy between January 2017 and January 2020 were included in the study. FNAB was performed on suspicious nodules according to the TIRADS classification. Nodules with "atypia/follicular lesion of undetermined significance (AUS/FLUS)", "non-diagnostic (ND)" cytology or "follicular neoplasm/suspicious for follicular neoplasm (FN/SFN)" according to FNAB were defined as "indeterminate cytology (IC)". Nodules were analyzed in two groups. Nodules with false negative FNAB were included in Group-1, while nodules with true positive and true negative FNAB were included in Group-2. Demographic and clinical data, pathologic results and genetic profiles of the patients were statistically compared for all patients and IC group separately.
 Results: The results of FNAB and final pathology were discordant in 94 patients (Group-1) and concordant in 233 patients (Group-2). In the IC subgroup, 56 of 95 patients were in IC/Group-1 and 39 patients were in IC/Group-2. The accuracy of FNAB was statistically significantly higher in the presence of extrathyroidal extension (71.4% vs. 30.8%), perineural/lymphovascular invasion (60.0% vs. 29.6%), classical variants (68.5% vs. 50.7%), non-encapsulated tumors (67.9% vs. 50.0%) and multicentricity (47.2% vs. 24.1%). In the IC group, the presence of thyroiditis (75.0% vs. 49.2%) and high serum Anti-TPO levels (60.0% vs. 30.7%) increased the rate of false negativity on FNAB. High serum Neutrophil to Lymphocyte Ratio (NLR) and small tumor size also increase the false negativity of FNAB, especially in IC group patients.
 Conclusion: The diagnostic accuracy of FNAB is increased in classical variant tumors and in tumors expected to be aggressive due to presence of extra-thyroidal extension, perineural/lymphovascular invasion, non-encapsulated tumors and multicentricity. It should be kept in mind that the false negative results of FNAB increase in the presence of thyroiditis, high level of serum anti-TPO and high level of NLR.
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