Baruj Benacerraf was born in Venezuela to Spanish Moroccan and Algerian parents. When he was 5 years of age, his family moved to Paris, France, where he received most of his primary education. The original plan was that Baruj would go into law and assist the family business in Venezuela, but then Hitler intervened. His family heard the distant drumbeat of war, and as they were Jews in Paris, his father had the foresight to move the family back to Venezuela in advance of Fall Rot, the Nazi invasion of France. As his schooling had been unexpectedly interrupted, Baruj was sent to the United States to complete his education. It was after his transfer to Columbia University that his interest in science was kindled and he decided to apply to medical school, rather than pursuing law. However, he had not appreciated how difficult a goal this would be for someone of his ethnic background at that point in history. Rejected from all the medical schools to which he had applied, he gained last-minute admission to the Medical College of Virginia only through the intervention of a friend's father.
The war again intervened when all medical students were drafted into the army; as part of this process, he became a naturalized US citizen. He was allowed to complete school and an internship at Queens General Hospital in New York City, then was called into active service late in the war and was stationed in France. Discharged at the age of 27, he had to decide what he would do next. He had a personal interest in immunology, having suffered asthma as a child, and he had experienced a taste of experimental science in medical school; these experiences persuaded him to try his hand at research. He applied to and was accepted into Elvin Kabat's laboratory for a postdoctoral fellowship and subsequently trained with Bernard Halpern in France. Once at the bench and making discoveries, he said “I was hooked for life as surely as if I had become addicted to heroin.”