Brain natriuretic peptide and N-terminal pro-brain natriuretic peptide are two well-established markers for cardiac failure in acquired heart disease. Nevertheless, the clinical utility of these markers in patients with congenital heart disease remains unclear. Therefore, the aim of this study was to evaluate the diagnostic and prognostic value of these markers in patients with congenital heart disease. A PubMed and EMBASE literature search was executed with focus on the most common simple congenital heart defects, atrial septal defect and ventricular septal defect. Data on brain natriuretic peptide measurement, cardiac function parameters, and follow-up were collected. In patients with atrial or ventricular septal defect, brain natriuretic peptide levels were mildly increased when compared with healthy age-matched controls. Shunt severity and pulmonary artery pressure correlated strongly with natriuretic peptide levels. A clear association between brain natriuretic peptide and functional class was demonstrated. After closure of the defect, a rise in brain natriuretic peptide levels in the first hours to days was observed. After longer follow-up, natriuretic peptide levels decreased and became comparable to pre-procedural values. In conclusion, this systematic review shows that brain natriuretic peptide levels are mildly increased in patients with unrepaired and repaired atrial or ventricular septal defect. Brain natriuretic peptide measurement might be a useful additional tool in the diagnostic work-up of patients with atrial or ventricular septal defect. Further investigation in a larger, prospective study with long-term follow-up is warranted to elucidate the true prognostic value of natriuretic peptides in patients with simple congenital heart disease.