V600E BRAF mutation is emerging as an independent marker of papillary thyroid carcinoma aggressive behavior. Papillary thyroid carcinomas harboring this mutation should be extensively resected. However, this requires an unquestionable cytological diagnosis of malignancy. Thus, cytological specimens should be properly handled to provide both morphological and molecular information. Here, we assessed whether our method of preparation of fine-needle aspiration material is suitable for both tests. A series of 128, routinely performed, fine-needle aspirations was analyzed. Each nodule was punctured three times. A representative Diff-Quik smear prepared from the first two passages was evaluated onsite. When microscopy was diagnostic (n = 44), the third needle pass was dedicated to harvest material for BRAF testing; in the remaining cases (n = 84), additional direct smears for cytology were prepared and the remaining material in the needle plus the needle rinsing was collected for BRAF testing. Cellularity was adequate in 126/128 (98%) cases. Cytological diagnoses were inadequate (2%), benign (85%), follicular lesion of undetermined significance (5%), follicular neoplasms (2%), suspicious for malignancy (2%), and malignant (4%). Higher average of extracted DNA concentration was observed in the dedicated pass group (25.9 vs 7.95 ng/microl). However, the rate of successful exon 15 BRAF amplification was similar with (43/44; 97.7%) or without (79/84; 94%) the dedicated pass. Thus, our protocol is suitable for both tests. Whenever necessary BRAF testing may also be performed on the residual samples of thyroid nodules, without interfering with routine cytology.