She was so good as a doctor that within three years she became head of the pediatric cardiac clinic at Johns Hopkins’ children hospital – the Harriet Lane Home. Now she had to meet another challenge. She began losing her hearing. She got a hearing aid and learned to read lips, but nothing helped her listen to little children’s hearts beating through her stethoscope. So, she learned to listen with her hands, gently placing her fingers on a child’s chest and feeling for murmurs.

Her specialty became congenital heart defects. While rare, there are quite a few types of malformed hearts babies may have.  Some they grow out of, others lead to death if not fixed. With  improved chest x-rays and EKG’s she was able to keep records of baby’s hearts while they lived and then if they died, note the malformations from autopsies. Taussig became particularly interested in blue baby syndrome, also known as tetralogy of Fallot. These babies have a malformed heart that prevents them from getting enough oxygen, causing them to turn blue. These children often died as infants, and those that survived longer could be confined to wheelchairs.

Taussig discovered that blue babies had decreased pulmonary blood flow to the lungs, reducing available oxygen throughout the body. As she observed the surgery of another heart defect, she thought of a solution. This surgery had the opposite problem of blue babies. Too much blood was cycled through the lungs due to an artery failing to close properly. In 1939 when she watched a doctor attempting to correct this problem by removing a duct (an extra blood vessel connecting two arteries), she realized adding a duct might solve blue babies lack of oxygen. She went to the surgeon and asked him to consider adding such a duct. He viewed her idea as a pipe dream and refused to look into it.

The idea didn’t leave her and in 1942 she observed Dr. Alfred Blalock perform the same surgery. Afterward she sought him out and said, “Dr. Blalock, you’ve done a very nice job closing this ductus; why can’t you build a ductus?...To some of our cyanotic children, it would mean a life for them.”

Blalock didn’t totally dismiss the idea, but set up a meeting between Taussig, himself and his surgical technician, Vivien Thomas. Thomas remembered the meeting in his autobiography:

• Helen passionately described her patients and their plight and that no known medical treatment existed. She went on to suggest that their only hope was a type of surgical approach to ‘get more blood to the lungs,' as a plumber changes the pipes around.

The challenge was accepted and the three began working on the problem. Vivien Thomas set about learning how to re-arrange the blood’s plumbing by operating on dogs, who had blood vessels twice the size of a sick child. Two years later, they were ready and Dr. Blalock performed the first surgery with Thomas hovering behind him. Sitting in the gallery was Taussig.

The surgery was incredibly complicated and delicate with the 15-month-old girl’s small blood vessels. The idea was to join the pulmonary artery to a systemic artery carrying oxygenated blood. It seemed to work. The little girl’s skin became pink and she survived for two months, before dying. But thereafter, the successes came. Soon, parents were bringing their blue babies from all over the country. So Taussig and Blalock started traveling all over the world, teaching doctors how to perform the operation.

Vivien Thomas, due to being an African-American, was left behind and also left off their published results, and left off the name given to the procedure – the Blalock-Taussig shunt. Only much later did doctors begin referring to it as the Blalock-Thomas-Taussig shunt to recognize that it was a three-person collaboration that cured blue babies. It became a standard operation with a 99% success rate for one year survival, and a 95% success rate for 25 year survival.