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Objective The aim of this study was to identify predictive factors for pathologic central lymph node metastasis (CLNM) in patients with clinically negative CLNM (cN0) papillary thyroid microcarcinoma (PTMC) to suggest a specific group of cN0 PTMC patients who benefit from prophylactic central lymph node dissection (CLND). Background PTMC have excellent prognosis, however, 8% have recurrent disease. Recurrence is associated with regional lymph node metastasis. It has been reported that pathologic CLNM is found in 30 to 65% of cN0 PTMC patients. However, prophylactic CLND for cN0 PTMC remains controversial. Methods We reviewed the records of papillary thyroid carcinoma patients with a tumor size on preoperative ultrasonography (US) of ≤10 mm and negative CLNM on preoperative physical examination, US, and positron emission tomography/computed tomography (PET/CT), who underwent total thyroidectomy or thyroid lobectomy with prophylactic CLND between April 2010 and February 2013. In total, 163 patients were included. We evaluated the relationship between preoperatively assessable factors including age, gender, body mass index, preoperative metformin use, primary tumor size through preoperative US, the maximum standardized uptake value (SUVmax) of the primary tumor through preoperative PET/CT, and the bilaterality of the primary tumor and pathologic CLNM. Results A SUVmax of the primary tumor of >3 was an independent preoperatively assessable factor predictive of pathologic CLNM in cN0 PTMC patients. Conclusions Prophylactic CLND might be considered in cN0 PTMC patients with a SUVmax of the primary tumor of > 3 to reduce the risks of residual CLNM and recurrence.