Background: Thyroid disease affects about 5% of the World’s population. Fine Needle Aspiration Cytology (FNAC) helps in planning extent of surgery. In some studies, FNAC has been found to have a low accuracy for malignancy.

Objective: To estimate the sensitivity and specificity of FNAC in detecting malignancy for thyroid disease using histopathology as the gold standard.

Methods: Patients who underwent clinical and laboratory evaluation and thyroidectomy at Mulago National Referral hospital and the Pathology department of Makerere University College of Health Sciences were consecutively recruited over a four months period. Analysis using STATA version 10 focused on sensitivity, specificity and accuracy of FNAC in detecting malignancy.

Results: In total, 99 patients were recruited, the F:M ratio was 15.5:1 and median age was 42 years (IQR 34-50). The median duration of symptoms was 364 weeks (IQR 104-986). The proportion of patients with malignancy was 13.3% with papillary thyroid carcinoma being the most predominant type and colloid goiter was the most predominant benign thyroid disease. The sensitivity was 61.5% and specificity 89.5% .

Conclusion: This study revealed high specificity and low sensitivity of Fine Needle Aspiration Cytology (FNAC) at detecting malignancy in thyroid nodules