In 1918, Lyster established an army laboratory that put aviation medicine on a sound scientific basis in the United States and he insisted on making military aviation physicians organic members of the flying squadrons, thus creating the position and role of "flight surgeon".

It was by War Department Special Order 207 (September 6, 1917) that Lyster became the first chief surgeon, Aviation Section, Signal Corps, United States Army—a position he had recommended as essential to fully realize the capability of Army aviation and provide adequate medical support to it.

Following a visit to Europe in 1918, Lyster conducted numerous research studies on the "Care of the Flyer" which led to substantial improvements in treatment and recovery.

Learning from the British experience during the first years of World War I, Lyster made two important contributions to the efficiency and safety of flying.

This program was under the control of a board "with discretionary powers to investigate all conditions affecting the physical efficiency of pilots, to carry out experiments and tests at different flying schools, to provide suitable apparatus for the supply of oxygen ... [and] to act as a standing organization for instruction in the physiological requirements of aviators."

This board established the first laboratory of its kind and put aviation medicine on a sound scientific basis in the United States.

This arrangement meant that surgeons familiar with aviation would deploy with the flying units, rather than being part of a larger medical organization that would be slower to respond.

[4] After the death of Dr Gorgas, Lyster carried on his work with the Rockefeller Foundation (1920–24) of eliminating yellow fever from Mexico and Central America.