We investigated MBL2 and MASP2 genotypes, serum MBL (mannose-binding lectin) levels and activities of its complexes with associated serine proteases (MASP-1, MASP -2), in relation to complications following cardiac surgery in 195 children. The incidence of SIRS was lower in patients carrying MBL2 A/O and O/O genotypes (p = 0.024). Children with MBL levels <500 ng/ml had a lower risk of SIRS (p = 0.014) and fever (p = 0.044). Median MBL concentration was higher in patients who developed SIRS (p = 0.048) but lower in those with post-operative infections (p = 0.046). MBL-MASP-2 activities <100 mU/ml protected from SIRS (p = 0.007), low cardiac output syndrome (p = 0.03) and multiorgan failure (p = 0.012). In contrast, MBL2 YA/YA genotypes were associated with SIRS (p = 0.018), low cardiac output syndrome (p = 0.018), fever (p = 0.018) and high inotropic score (VIS >30) (p = 0.021). Thus, low MBL concentrations and associated genotypes may protect patients from systemic inflammation while high MBL serum levels and corresponding genotypes are risk factors of postoperative complications.