This study aimed to evaluate the diagnostic value of BRAFV600E mutation and DNA ploidy determination for Papillary Thyroid Micro-Carcinoma (PTMC) through fine-needle aspiration. Clinical data, including histology, patient population statistics and clinical results were gathered. Patients’ thyroid-micro-lesions were made into FNA-stained smears, DNA was extracted from the smears for different cytological diagnoses. BRAFV600E mutation was detected by Amplification Refractory Mutation System (ARMS). DNA ploidy determination of PTMC was detected by DNA quantitative analyser. All surgical cases were collected for histopathological diagnosis. BRAFV600E mutation was identified in 168 of 180 (93.3%) of PTMC, 0/9 of thyroid follicular carcinomer and 0/1389 of benign thyroid nodules. 127/180 (70.5%) patients got a definitive diagnosis of PTMC when only use cytology. 177/180 (98.3%) patients got a definitive diagnosis of PTMC by a combination of cytology and BRAFV600E mutation analysis (p<0.05). DNA ploidy determination showed no abnormal on papillary thyroid microcarcinoma. BRAFV600E mutation could be only detected in Papillary Thyroid Carcinoma (PTC) patients and is the most common oncogenic alteration in PTC patients. Thus BRAFV600E mutation is a genetic marker of PTMC. BRAFV600E mutation analysis via fine-needle aspiration improved 27.8% of the diagnosis rate of PTMC when combined with cytology.