Background: The diagnostic limitations of fine needle aspiration (FNA), like the "indeterminate" category, can be partially overcome by molecular analysis. As PAX8/PPARG and RET/PTC rearrangements have been detected in follicular carcinomas (FTC) and papillary carcinomas (PTC), their detection in FNA smears could improve FNA diagnosis. To date, these rearrangements have never been analyzed in routine air-dried FNA smears, but only in frozen tissue, formalin-fixed paraffin-embedded (FFPE) tissue, and in fresh FNA material. Fixed routine air dried FNA samples have hitherto been judged as generally not suitable for testing these rearrangements in a clinical setting. Therefore, the objective of the present study was to investigate the feasibility of extracting RNA from routine-air-dried FNA smears for the detection of these rearrangements with RT-PCR. Methods: A new method for RNA extraction from routine air-dried FNA smears was established which allowed analysis for the presence of four variants of PAX8/PPARG and RET/PTC 1 and RET/PTC 3, which were analyzed in 106 routine FNA smears and the corresponding surgically obtained FFPE tissues using real time-qPCR (RT-qPCR). In order to assess RNA quality, an intron-spanning PAX8 cDNA was amplified. Results: Acceptable RNA quality was obtained from 95% of the FNA samples and 92% of the FFPE samples. PAX8/PPARG was detected in 4 of 96 FFPEs and in 6 of 96 FNAs. PAX8/PPARG was present in 4 of 10 FTC and in 3 of 42 follicular adenomas (FA). Similarly, RET/PTC was found in 3 of 96 FFPEs and in 4 of 96 FNAs. Two of 21 PTC samples and 3 of 42 FA samples carried this rearrangement. Conclusion: These data are the first to show the feasibility of extracting RNA from routine air dried FNA smears for the detection of PAX8/PPARG and RET/PTC rearrangements with RT-qPCR. These promising methodological advances, if confirmed in larger series of FNA and FFPE samples, may lead to the introduction of molecular analysis of routine air dried FNA smears in everyday practice.