In January 1938, Apgar returned to Presbyterian Hospital and Columbia University College of Physicians and Surgeons as director of a new Division of Anesthesia within the Department of Surgery with a joint appointment to the P & S clinical faculty. She and Allen Whipple had sketched the organization of the new division several months earlier. Their plan called for anesthesia services provided by ten anesthesiology residents, serving from one to three years, plus four senior medical students and one surgical intern. Residents would gradually replace the hospital's fourteen nurse-anesthetists as they vacated positions to marry or relocate. The division would focus first on clinical anesthesia, then start teaching medical students in September of 1938, and finally phase in a research program after the teaching program was established. For the first several years Apgar was the new division's only full-time staff member. Her responsibilities were daunting: coordinating anesthesia administration at Presbyterian, which performed nearly 5,000 general surgeries (i.e., not including the cases on obstetrics, pediatric, and other wards) during her first year there; recruitment and training of anesthesiology residents, teaching medical students who rotated through the anesthesia service, and initiating anesthesia research at the hospital. She also served as consulting anesthesiologist and clinical instructor at several other area hospitals.
Of necessity, Apgar did much of the teaching herself, and became a legendary and much-loved clinical instructor. There were no proper anesthesia textbooks at the time, so she and nurse-anesthetist Anne Penland compiled a handbook, "Notes on Anesthesia," for students' use, which went through several editions during the 1940s and 1950s. Much of her teaching was informal, done on clinical rounds at the bedside or in the hallway in an enthusiastic, outgoing style. L. Stanley James, who collaborated with Apgar for many years, noted that she was the one person the medical students never forgot. Quite uninhibited, she could talk about any part of the body without embarrassment, and often had students palpate her own tailbone (which had an unusual angle) to teach them about spinal anesthesia. Her standard visual aid was an old skeleton, the pelvis of which she used to demonstrate regional anesthesia. Resuscitation is an important part of anesthesia training, and Apgar insisted that students be prepared to apply their skills both inside and outside the hospital. She always carried a penknife (for emergency tracheostomies), an endotrachial tube, and a laryngoscope with her, and she advised her students to do the same. "Nobody, but nobody, is going to stop breathing on me!," she often said.
Apgar faced many challenges in establishing the new division, some imposed by professional or bureaucratic inertia, and others brought by the special circumstances of World War II. Recruitment of anesthesiology residents was difficult at first because of the low status of anesthesiology. The specialty was growing, and most medical anesthesiologists were male (Apgar had been the only woman resident in her training group at the University of Wisconsin), but many physicians still regarded it as nurses' work, not a proper medical specialty. Apgar had only two residents during the first year. She slowly increased their numbers in subsequent years, but several times was prevented from adding more because the hospital had no available residents rooms in which to house them. (Medical residents at the time were actually resident in the hospital where they served.) Older ideas about anesthetists also produced tensions with surgeons in the operating room: surgeons, accustomed to being the sole medical authority in the OR, sometimes had difficulty accepting anesthesiologists as their equals and acknowledging their superior expertise in anesthesia administration. Related to this was the problem of adequate financial compensation for anesthesiologists. Apgar had suggested from the start that they be paid ten percent of the surgeon's fee. Anesthesia at many other hospitals was considered a consulting service, like radiology or pathology, and the consultants could charge a professional fee. At Presbyterian, however, physicians giving anesthesia were not allowed to charge separate professional fees, a holdover from the days when nurses administered anesthesia. Apgar lobbied for several years to change this custom at Presbyterian, arguing that it was detrimental to the growth of the specialty and to the operation of her division.
Finally, there were the day-to-day realities of an overwhelming clinical load. Between 1933 and 1939, the number of patients given anesthesia yearly at Presbyterian and its associated clinics had increased from 7,849 to 9,944, yet there had been no corresponding expansion of the anesthesia staff. The residents were also called on to help with treating intractable pain, administering nerve blocks, and performing resuscitation, which could limit the time available to attend surgeries. Finally, Apgar's plan to improve the quality of anesthesia service required that staff members visit their patients before and after surgery. This increased the amount of time spent with each patient, and often improved surgical outcomes, but meant that each anesthesia staff member attended fewer patients in a given day. As the United States prepared to enter World War II, many physicians and nurses enlisted in the armed forces; the trend accelerated after the attack on Pearl Harbor in 1941, and Apgar's staffing situation became dire. Added to this were technical problems stemming from changes in surgical practice and anesthesia technologies. For example, the most popular general anesthetic, cyclopropane (introduced in 1929) was also quite combustible, and sometimes caused explosions in the OR when static electricity ignited it. For a time, the department of surgery discontinued its use rather than take the risk.
The end of World War II relieved the staffing shortages and recruitment problems, as physicians returned to civilian practice, many of them with fresh interest in anesthesiology. In 1945, for the first time, more anesthesia was administered by doctors than by nurses at Presbyterian. The number of nurse-anesthetists declined rapidly, as anesthesiology gained national recognition as a bona fide medical specialty. Under Apgar's direction, the anesthesia division had developed solid clinical and teaching programs by the late 1940s. The research element that she and Whipple outlined in their original plan, however, was far from fully developed. The heavy clinical and teaching load imposed by wartime circumstances had left Apgar little time for conducting or supervising research. As discussions began about making the division into a separate department, her lack of formal research experience proved a liability. Having organized and developed the anesthesia division, Apgar could reasonably expect to lead it into its next phase. But in 1949, Emanual Papper, a Bellevue anesthesiologist with a research background, was made chief of the division, and became the chair of the new department of anesthesia six months later. Apgar was appointed professor of anesthesiology, however, making her the first woman full professor at Columbia's College of Physicians and Surgeons.