Introduction: Surgical site infections (SSI) are an important cause of morbidity in pediatric cardiac surgery. Risk factors in patients requiring delayed sternal closure (DSC) are unknown. Aim: To report the rate of SSI in children undergoing cardiac surgery with DSC and determine the risk factors. Methodology: A retrospective case-control study, in patients younger than 15 years old undergoing cardiac surgery with DSC in our center between 2009 and 2010. SSI was diagnosed according to the criteria of the nosocomial infections committee of our institution, based on international recommendations. Univariate and multivariate analysis of variables was performed. A p < 0.05 was considered significant. Results: 58 patients were included; the average age was 9.5 days. The most frequent diagnosis were transposition of the great arteries (36%) and hypoplastic left heart syndrome (27%). 13 patients had SSI (22%); 11 incisional and 2 mediastinitis. It was independently associated to SSI by-pass (BP) time longer than 200 min (OR adjusted = 9,53; IC 95% 1,37-66,35) and mechanical ventilation (MV) more than 5 days (OR adjusted = 8,98; IC 95% 1,16-69,40). Conclusion: The duration of BP and MV are risk factors of SSI in children undergoing cardiac surgery with DSC.