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Background and objective With the rapid development of technology, stereotactic radiotherapy has been widely used. In a cohort of medically operable non-small cell lung cancer patients receiving stereotactic body radiation therapy (SBRT) survival rates “potentially equivalent to those of surgery” have been reported. Removing the field flattening filter, Clinac is capable of delivering dose rates much higher than conventional linac as well as reducing the treatment time. The goals of this work were to report safety and efficacy of SBRT treatment using a flattening filter-free model for non-small cell lung cancer (NSCLC) with small lesions. Methods From December 2011 to December 2013, 31 NSCLC patients who were T1-2N0M0, solitary pulmonary recurrence after surgery, and stage IV with oligo metastasis were enrolled, receiving SBRT treatment (60 Gy/8 f or 48 Gy/4 f) applying a flattening filter-free model. Results Compared with conventional technique, flattening filter-free model shortened the treating time with equivalent target dose and normal tissue dose. The median follow-up time is 19.4 mo. The 1-yr local control, regional control, distant control, progression free survival and overall survival rates were 96.8%, 96.8%, 83.9%, 77.4% and 96.8%. The most common side effects were radiation pneumonitis (29% grade 1, 3.2% grade 2) and chest pain (12.9% grade 1, 6.5% grade 2). Conclusion The use of flattening filter-free model in SBRT for small lesions of NSCLC patients is safe and effective. Long time follow-up and additional studies are still needed to validate our conclusions.