Differentiation of thyroid follicular lesions from parathyroid lesions on fine needle aspiration cytology can be very challenging, both being endocrine lesions with overlap in cytomorphologic features. In some cases, it may be impossible to differentiate thyroid neoplasms from parathyroid neoplasms based on cytologic grounds alone. Clinical information, including laboratory and radiologic findings, is crucial in these difficult cases. Immunocytochemistry is a useful diagnostic tool in differentiating thyroid from parathyroid neoplasms. In this case report, we detail the challenges faced in differentiating a parathyroid lesion from a thyroid follicular lesion based on cytomorphology, and how clinical information and immunocytochemistry were applied towards making a correct diagnosis.