We sought to evaluate the impact of prenatal diagnosis on morbidity and mortality in single ventricle (SV) lesions. All consecutive patients with pre- or postnatally diagnosed SV physiology admitted to our centre between January 2001 and June 2013 were reviewed. Primary endpoints included survival until 30 days after bidirectional cavopulmonary connection (BCPC) without transplant or BCPC takedown. Prenatal diagnosis was performed in 160 of 259 cases (62%). After excluding all cases with termination of pregnancy, intrauterine demise or treated with comfort care, a total of 180 neonates were admitted to our centre for treatment, including 87 with a prenatal and 93 with a postnatal diagnosis. Both groups showed similar distribution regarding diagnosis, dominant ventricle and risk factors such as restrictive foramen or some form of atrial isomerism. A larger proportion of postnatally diagnosed children presented at admission with elevated lactate > 10 mmol/l (p = 0.02), a higher dose of prostaglandin (p = 0.0013) and need for mechanical ventilation (p < 0.0001). Critical lesions such as hypoplastic left heart syndrome were an important determinant for morbidity and mortality. Thirty-days survival after BCPC was better in patients with prenatal diagnosis (p = 0.025). Prenatal diagnosis is associated with higher survival in neonates with SV physiology.