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Purpose This study aimed to evaluate the associations between mitochondrial dynamics related genes - MFN1, MFN2 and DRP1 polymorphisms and risk of lung cancer. Methods Six polymorphisms of MFN1, MFN2 and DRP1 were genotyped in 600 cases and 600 controls using a MassARRAY platform. Results The MFN1 rs13098637-C and DRP1 rs879255689-A alleles were associated with an increased risk of lung cancer ( p rs13098637 =0.004, p rs879255689 =0.005), while MFN2 rs4240897-A and rs2236058-G were related to a decreased risk of disease ( p <0.001). The rs13098637-TC/CC and rs879255689-GA/AA were determined as risk genotypes for lung cancer ( p rs13098637 =0.014, p rs879255689 =0.013), whereas the rs4240897-GA/AA and rs2236058-GG were identified as protective genotypes against lung cancer risk ( p <0.001). Genetic model analysis showed that rs13098637 was correlated with an elevated risk of lung cancer in dominant and log-additive models ( p dominant =0.007, p log-additive =0.004). Moreover, rs879255689 was associated with an increased risk of disease in all three models ( p dominant =0.014, p recessive =0.028, p log-additive =0.005). In contrast, rs4240897 and rs2236058 were related to reduced risk of disease in all three models (rs4240897: p all <0.001; rs2236058: p dominant =0.008, p recessive <0.001, p log-additive <0.001). In addition, these associations were related to the smoking status and pathological type of lung cancer patients. Conclusion These results shed new light on the association between mitochondrial dynamics related genes and risk of lung cancer.