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Abstract To assess the efficacy, safety, and feasibility of a separate inserted positioning fine needle-mediated breathing-control technique applied to computed tomography (CT)-guided percutaneous puncture for biopsy or microwave ablation (MWA) of small lung/liver nodules near diaphragm. Total 46 patients with pulmonary/liver small nodules (≤ 3 cm in size) near diaphragm(nodule within 1 cm distance to the diaphragm)were undergone percutaneous biopsy ( n = 15) or MWA (n = 31) under the guidance of CT, and a separate positioning fine needle-mediated breathing-control technique was applied for the precise punctures. CT plain scan was performed to monitor the complications after the procedure. The patient baseline data, operation details, successful rate, major complications as well as radiation dose during the procedure were recorded and analyzed. With the assistance of a fine positioning needle insertion for controlling the breathing, the puncture success rate for biopsy or MWA reached 91.30% (42/46). For biopsy, the mean nodule diameter, nodule distance to the diaphragm, puncture time and radiation dose during CT scan were 2.27 cm ± 0.74, 0.61 cm ± 0.24, 18.67 min ± 6.23, 28.84 mSv ± 6.99, respectively; For MWA, the mean nodule diameter, nodule distance to the diaphragm, puncture time and CT radiation dose were 2.35 cm ± 0.64, 0.69 cm ± 0.23, 38.71 min ± 13.65, 33.02 mSv ± 8.77, respectively. Totally, there were three and four cases found minimal puncture-related hemoptysis and pneumothorax needed no additional treatments, respectively. We recently developed and verified a feasible, safe and highly effective puncture technique with reasonable radiation dose for CT-guided biopsy or MWA for small nodules abutting diaphragm, therefore worthy of extensive application to similar clinical situations.