Introduction: We evaluated the clinical performance of an expanded mutation panel in combination with microRNA classification (MPTX) for the management of indeterminate thyroid nodules. Methods: MPTX included testing of fine needle aspirates with a combination of ThyGeNEXT® mutation panel for strong and weak driver oncogenic changes and ThyraMIR® microRNA risk classifier. MPTX test status (positive or negative) and MPTX clinical risk classifications (low, moderate, or high risk) were determined blind to patient outcomes. Surgical pathology and clinical follow-up records of patients from multiple centers were used to determine patient outcomes. MPTX performance was assessed by Kaplan Meier analysis for cancer-free survival of patients, with risk of malignancy determined by hazard ratios (HR). Results: Our study included 140 patients with AUS/FLUS or FN/SFN nodules, of which 13% had malignancy. MPTX negative test status and MPTX low risk results conferred a high probability (94%) that patients would remain cancer free. MPTX positive test status (HR 11.2, P<0.001) and MPTX moderate risk results (HR 8.5, P=0.001) were significant risk factors for malignancy, each conferring a 53% probability of malignancy. MPTX high risk results elevated risk of malignancy even more so, conferring a 70% probability of malignancy (HR 38.5, P<0.001). Conclusions: MPTX test status accurately stratifies patients for risk of malignancy. Further classification using MPTX clinical risk categories enhances utility by accurately identifying patients at low, moderate, or high risk of malignancy at the low rate of malignancy encountered when clinically managing patients with indeterminate thyroid nodules.