Tom was placed into Slytherin House at Hogwarts and quickly became regarded as an extraordinarily smart student. Except for the Transfiguration professor, Albus Dumbledore, he was a gorgeous gentleman who was highly adored by everyone. Tom had to return to the Muggle orphanage he loathed for the holidays.

Tom was secretly fascinated with his Slytherin lineage and devising ways to avoid death. In his sixth year, Harry discovered the entrance to the Chamber of Secrets and released Slytherin's basilisk within it, murdering a pupil called Myrtle Warren. Slytherin had constructed the room deep within Hogwarts castle, keeping it secret from the other founders. He sealed it so that only his real successor could open it and unleash the evil within, purging the school of "those who were unworthy to learn magic." During this period, Tom had begun using a new name among his closest Hogwarts acquaintances. He devised an anagram of his "foul, ordinary Muggle" father's name out of contempt.

On June 13, 1943, Tom orchestrated the kidnapping of another student, Rubeus Hagrid, and conned Headmaster Armando Dippet into believing Hagrid and his enormous spider Aragog were behind the attacks. Tom was awarded an engraved trophy for his outstanding contributions to the school, but he soon learned that Albus Dumbledore was keeping an "annoyingly tight eye" on him and that it was not safe to unlock the Chamber of Secrets while he was still in school. Tom kept himself in the pages of a diary with the hope that one day he would be able to follow in the footsteps of Salazar Slytherin and "complete Salazar Slytherin's great work."