To determine the correlation between the results of thyroid fine-needle aspirations interpreted using the Bethesda system and final histopathological reports for patients at an oncology hospital (OH) and non-oncology hospitals (NOHs).A retrospective, cross-sectional, descriptive study was performed to compare the cytology and histopathology results for patients with thyroid nodules in three Colombian hospitals. The final correlation of diagnoses between the two methods is reported. In Colombia, the health system provides the existence of general care hospitals and hospitals specializing in care of patients with cancer.A total of 196 reports were reviewed, of which 53% were from OH and 47% were from NOHs. A greater proportion of category V (37.5%) was diagnosed at the OH, whereas NOHs diagnosed a greater proportion of category II (42.3%). The global correlation between diagnoses made using cytology and histopathology was 93.3% for categories V and VI (based on the final malignant diagnosis) and 86.9% for benign category II. Significant differences between institution types were observed when category IV and V and malignant histopathology were compared (56.3% OH vs. 23.5% NOH; P = 0.05 for category IV, 97.4% OH vs. 82.3% NOH; P = 0.03 for category V), while no significant difference between institution types was observed when category II and final benign diagnosis were compared (P = 0.6).The Bethesda system for thyroid cytology correlates adequately with final histopathological diagnosis in Colombia. Significant differences were identified in the diagnostic correlation for malignant lesions between the OH and NOHs in categories IV and V caused by selection bias of the population.