Background: Fine-needle aspiration (FNA) is a useful diagnostic tool for preoperative evaluation of thyroid nodules. However, cytomorphology alone has poor accuracy for the diagnosis of lymphoproliferative disorders involving the thyroid. This study reviews our experience with flow cytometry on thyroid FNA and correlation with surgical follow-up at The Johns Hopkins Hospital. Methods: The 11,118 thyroid FNAs performed over a 20-year period were reviewed for clinical flow cytometry data (n = 62) or a subsequent diagnosis of lymphoma in the thyroid without flow cytometry data (n = 2). Result: Sixty-four cases (0.6%) were included out of 11,118 thyroid FNAs collected over a 20-year period. Lymphoma was diagnosed 13 times. In 8 cases, both cytomorphology and flow cytometry arrived at the correct diagnosis. Cytomorphology alone made the correct diagnosis twice in the absence of flow cytometric results; flow cytometry made the diagnosis once in the absence of suspicious morphology. Neither flow cytometry nor cytomorphology made the correct diagnosis in 2 sparsely cellular cases. Conclusion: The combination of cytomorphology and flow cytometry is a useful diagnostic modality for the work-up of lymphocyte-rich thyroid nodules that show atypical lymphocyte populations.