At birth, the ductus arteriosus is still open, and there is higher than normal resistance to blood flow in the lungs. This allows for adequate oxygenation via mixing between the atria and a normal appearance at birth. When the ductus begins to close and pulmonary vascular resistance decreases, blood flow through the ductus is restricted and flow to the lungs is increased, reducing oxygen delivery to the systemic circulation. This results in cyanosis and respiratory distress which can progress to cardiogenic shock. The first symptoms are cyanosis that does not respond to oxygen administration or poor feeding. Peripheral pulses may be weak and extremities cool to the touch.

HLHS often co-occurs with low birth weight and premature birth.

In neonates with a small atrial septal defect, termed "restrictive", there is inadequate mixing of oxygenated and deoxygenated blood. These neonates quickly decompensate and develop acidosis and cyanosis.

On EKG, right axis deviation and right ventricular hypertrophy are common, but not indicative of HLHS. Chest x-ray may show a large heart (cardiomegaly) or increased pulmonary vasculature. Neonates with HLHS do not typically have a heart murmur, but in some cases, a pulmonary flow murmur or tricuspid regurgitation murmur may be audible.

Co-occurring tricuspid regurgitation or right ventricular dysfunction can cause hepatomegaly to develop.

Common symptoms include a grayish-blue (cyanosis) coloration to the skin, lips, fingernails and other parts of the body. Other pronounced symptoms can be rapid/difficulty breathing, poor feeding, cold hands or feet, or being inactive and drowsy. "In a baby with hypoplastic left heart syndrome, if the natural connections between the heart's left and right sides (foramen oval and ductus arteriosus) are allowed to close, he or she may go into shock." Signs of shock can include cool or clammy skin, a weak or rapid pulse, and dilated pupils.

Hypoplastic right heart syndrome is a congenital heart defect in which the right atrium and right ventricle are underdeveloped. This defect causes inadequate blood flow to the lungs and thus, a blue or cyanotic infant.[3]

Hypoplastic left heart syndrome (HLHS) is a rare congenital heart defect in which the left side of the heart is severely underdeveloped. It may affect the left ventricle, aorta, aortic valve, or mitral valve.

Fetal aortic stenosis is a disorder that occurs when the fetus’ aortic valve does not fully open during development. The aortic valve is a one way valve that is located between the left ventricle and the aorta, keeping blood from leaking back into the ventricle. It has three leaflets that separate when the ventricle contracts to allow blood to move from the ventricle to the aorta. These leaflets come together when the ventricle relaxes.

Fetal aortic valve stenosis can be diagnosed by echocardiography before birth. The diagnostic features include a poorly contracting left ventricle, aortic valve thickening/restriction, a varying degree of left ventricular hypertrophy and abnormal Doppler flow characteristics in the left heart. There may be little or no detectable flow into or out of the left side of the heart.

There are two screening periods, one during the first trimester and the other during the second trimester. Fetal aortic stenosis is typically detected between 18 and 24 weeks gestation. This early detection is important because it allows for parents to be counseled in a timely and rational manner, allowing for discussion of prognosis and possible outcomes. Another reason for this crucial early detection is because it allows for postnatal management planning.