When Heisenberg first arrived in Munich, the 18-year-old was still planning to study pure mathematics. However, after a disastrous meeting with a renowned and intimidating professor, he felt he had to seek alternatives. He came to Ernest Sommerfeld, who would be his first scientific mentor. Sommerfeld was a natural teacher who supported his students wholeheartedly. When inflation put students in financial trouble–a frequent occurrence–Sommerfeld would help them out with his own funds. At the time, Sommerfeld, a theoretical physicist, was low on the academic hierarchy. All the school's resources went to the Nobel Prize-winning experimental physicist Willy Wien. Upon Heisenberg's arrival, however, the trends began to change.

If Heisenberg's father figure was Sommerfeld, then his older brother was Wolfgang Pauli. Pauli was only one year older, but had come to Munich with even more advanced training in physics than Heisenberg. He had arrived having already written a paper on general relativity, ready for publication. Pauli and Heisenberg were very different in temperament. The former was outspoken and aggressive, with an exciting social life, while the latter was quiet and often withdrawn, always diligent. As physicists, their mutual impact was great, as each pushed the other along toward his achievements. Though they were together in Munich only briefly, they kept in touch for the rest of their lives. Their collected letters constitute a great chapter in modern physics.

At the time of Heisenberg's arrival in 1920, Sommerfeld had already been engaged with one central problem: how to explain the behavior of spectra emitted by atoms. Atoms stimulated by energy would emit not an entire spectrum of radiation, but only specific lines corresponding to certain frequencies that were characteristic of whatever element the atom was. Moreover, x-ray spectroscopy posed two problems that had to be resolved. First was the problem of the lines splitting into doublets and triplets of lines, called multiplets. Second was the fact that these multiplets turned into a regular pattern of lines when the atom was exposed to a magnetic field. This anomaly was known as the Zeeman effect.

Four weeks after Heisenberg's arrival, Sommerfeld invited him to take a look at the Zeeman effect data. Within a year Heisenberg proposed his atomic core model, which seemed to explain many of the observed phenomena but failed to satisfy the requirements of previously accepted theories that Niels Bohr and Sommerfeld had established. Although Bohr and Sommerfeld had themselves departed from classical mechanics, they held firm to certain principles of quantum theory–principles that Heisenberg's model clearly violated. For instance, Heisenberg had used half-integer quantum numbers whereas quantum theory always required whole integers. Nevertheless, Heisenberg's was the only model that could reconcile the Zeeman effect with quantum physics.

Nearly everyone in the scientific community reacted to Heisenberg's ideas with disapproval. His model showed promise, but scientists like Bohr and even Sommerfeld, who had encouraged the model's publication, ultimately disagreed. The scientists were especially bothered by Heisenberg's discarding of certain principles that were fundamental to their own work. Years later, however, many of the characteristics of Heisenberg's model would be justified by new discoveries, in particular Heisenberg's own quantum mechanics.

Over fifteen years older than Heisenberg, Bohr played a pivotal role in his development. Bohr, often cited next to Einstein as the most important physicist of the twentieth century, had come along shortly after scientists like Max Planck to extend our understanding of the atom. Perhaps just as important was his role as mentor, not just to Heisenberg, but to physicists all over the world. Planck had founded and led the Copenhagen Institute, which had become the world's leading center for theoretical physics research. Though Bohr and Heisenberg may have met earlier, their first chance to talk at length came in June 1922, when Bohr was delivering a series of lectures at the Göttingen physics institute. As they walked along the hills overlooking the town, Heisenberg and Bohr discussed not just science but also the philosophical questions that surrounded the atom–questions that would concern Bohr perhaps more than any other scientist of his time. Moreover, Bohr's peaceful and kind manner always softened his intellectual criticism, as he and Heisenberg did differ fundamentally. Soon, Heisenberg was writing back to his parents with glowing praise of the mentor he had just found.