This study was designed to determine if routinely prepared thyroid FNA cytology smears can be used for molecular profiling by NGS for oncogene mutations and oncogenic fusion transcripts, and by a microRNA expression classifier. Molecular test results of cytology smears were compared to samples collected in RNARetain^® from FNA samples collected from the same patient, same nodule, and during the same FNA procedure. Of the 94 thyroid FNA samples tested (47 mutational analyses, 47 microRNA classifier assessments based on a validated 10 marker panel) only 5 samples showed discordant results. Comparison of test results obtained using the 2 specimen types from the same patients demonstrated 98% concordance between the results of NGS-based mutation sequencing tests and 90% concordance between the results of microRNA expression-based tests. Study results demonstrate that both the FNA in RNA stabilizing solution (RNARetain^®) and the FNA smears on the cytology slides can be successfully used in the dual-platform molecular diagnostic testing for mutational change and microRNA expression-classification of thyroid nodules.