This study examined a comprehensive evaluation of miRNA gene expression in diverse thyroid lesions (n=534) and developed predictive models for the classification of thyroid nodules. miRNA-based classifiers complemented and significantly improved the diagnostic performance of the 17-mutation panel (P<0.001 for McNemar’s tests). In a subset of resected tissues (n=54) and in an independent set of thyroid nodules with indeterminate cytology (n=42), the optimized ThyraMIR® miRNA Classifier increased diagnostic sensitivity by 30% to 39% and correctly classified 100% of benign nodules as negative by the 17-mutation panel. In contrast, testing with broad-targeted next-generation sequencing panels decreased diagnostic specificity by detecting additional mutations of unknown clinical significance in 19% to 39% of benign lesions. The study results demonstrate that, independent of mutational status, miRNA expression profiles are strongly associated with altered molecular pathways underlying thyroid tumorigenesis, and combined testing for miRNA gene expression and well-established somatic gene alterations is a novel diagnostic strategy that can improve the preoperative diagnosis and surgical management of patients with indeterminate thyroid nodules.