FNA Reader is a clinical decision support tool that assists healthcare providers in appropriately working up thyroid nodules based on the 2009 American Thyroid Association (ATA) Guidelines and The Bethesda System for Reporting Thyroid Cytopathology. It includes recommendations for the initial workup of thyroid nodules based on TSH level, radionuclide scan and/or thyroid ultrasound. By entering the ultrasonographic characteristics of the thyroid nodule, users can learn whether thyroid fine needle aspiration (FNA) is indicated in a particular patient, and what is the strength of the evidence supporting the recommendation. How the FNA result is managed will depend on the specific pathology interpretation of the FNA, as each diagnostic category is associated with a certain risk of malignancy, all of which are summarized in FNA Reader.