Objective:To compare the impacts of different sample collection methods and RNA extraction methods from thyroid fine needle aspiration samples on the results of target gene detection. Methods:Trizol and RNeasy Plus Micro Kit (Qiagen) were used to extract RNA from thyroid FNA samples obtained from a separate puncture or leftover material in the needle; the thyrocyte-relevant genes were detected by reverse transcription-polymerase chain reaction; and the influence of different sample types and RNA extraction methods on RNA quality,quantity and RT-PCR outcome was analyzed. Results:RNA was isolated from 102 FNA samples,the RT-PCR results showed that the positive detection rate of GAPDH and TG were 97.06% and 93.14% respectively,followed by TPO,TSHr,and NIS. The concentration and quantity of RNA extracted by Trizol were higher than that by RNeasy Plus Micro Kit in samples from a separate puncture,but the differences were not statistically significant(P > 0.05). The OD ratio of RNA extracted by the two methods had no significant difference,so as the success rate of RT-PCR(P > 0.05). In samples obtained from leftover material in the needle,no significant differences were found in RNA concentration,quantity,OD ratio and success rate of RT-PCR between the two RNA extraction methods (P > 0.05). In the group that RNA was extracted by Trizol,there were no significant correlation between sample collection methods and RNA concentration,quantity,OD ratio or success rate of RT-PCR (P > 0.05). The same results were observed in the group that RNA was extracted by RNeasy Plus Micro Kit,different sample collection methods had no significant impact on RNA concentration,quantity,OD ratio and success rate of RT-PCR (P > 0.05). Conclusion:RNA can be successfully isolated from FNA samples to detect genes. Samples from a separate puncture or leftover material and RNA extraction methods of Trizol or Qiagen can all be used in RNA extraction from thyroid FNA samples.