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Surgical site infection (SSI) in thoracic surgery remains a significant cause of morbidity and prolonged hospitalization. Minimally invasive surgery (MIS) has significantly reduced the risk of SSI. We intended to compare whether there was difference between video-assisted thoracic surgery (VATS) and robotic-assisted thoracic surgery (RATS) in SSI and highlight possible factors influencing SSI in lobectomy.This retrospective study analyzed patients who underwent minimally invasive lobectomy from January 2018 to December 2019. All patients' clinical characteristics and surgery-related information which may be related to the likelihood of SSI were recorded.A total of 1231 patients' records were reviewed with 806 VATS and 425 RATS. SSI was classified as deep or superficial SSI. Eighty-six (7.0%) patients were found to develop an SSI with 62 patients having deep infections and 24 had superficial infection. No statistical difference in the incidence rate and category of SSI was observed between patients undergoing VATS and RATS.There was no difference in the incidence of SSI between VATS and RATS lobectomy. Male gender, heavy smoking, uncontrolled diabetes mellitus, body mass index (BMI) 27.9, more blood loss, and the higher National Healthcare Safety Network (NHSN) risk index score (1 or 2) were the independent risk factors of SSI following minimally invasive lobectomy, while male gender, uncontrolled diabetes mellitus, BMI 27.9, more blood loss and the higher NHSN risk index score (1 or 2) were the main predictors of deep SSI.