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Gertrude ("Trudy") Elion was born in New York City on January 23, 1918. Her father, Robert Elion, a dentist, had immigrated to the United States from Lithuania at the age of 12. Her mother, Bertha Cohen, came to America alone at the age of 14 from the part of Russia that is now Poland; studying English at night school, she worked in the needle trades before marrying Robert at 19.

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When asked who had inspired and influenced her the most, Elion named her mother. A housewife with no higher education, Bertha Cohen Elion likely felt deprived that she had never been able to have a career of her own. She had great common sense and always wanted her daughter to have a career of her own. She was always very supportive of Elion in all her endeavors.

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Elion's report card reflects her early abilities in a wide range of subjects. Her one consistently low grade was in Physical Education; later, in college, she received straight As with the exception of one C in Physical Education.

From a very young age, Trudy displayed the qualities that would lead her to a Nobel Prize. Even before she started school, she wished to learn about the world around her. A voracious reader with "an insatiable thirst for knowledge," she was interested in everything around her. "It didn't matter if it was history, languages, or science," she later recalled. "I was just like a sponge."

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As a student at the all-girls Walton High School in the Bronx, Elion was not yet focused on science. Exploring history, writing, and performing, she received the school's Cooperation in Government Award and a prize in American history; belonged to the History Dramatic Club, the Electron Science Club, and the Glee Club; and published an essay and a poem in the yearbook. Propelled by her quick intelligence, she skipped two grades and graduated from high school in 1933, at the age of 15.