Alfons Popiełuszko passed his high school exams in 1965 and subsequently joined the Metropolitan Higher Seminary in Warsaw. This choice was no accident, it was because Cardinal and Primate of Poland, Stefan Wyszynski, was the senior pastor. Popiełuszko tried to stay close to the Primate following his footsteps to learn the Cardinal’s approach towards people. In particularly the Primate's dignified attitude during the millennial celebrations in 1966 left a lasting impression.
During his studies – although contrary to an agreement between the Church and the Communist state - he was called up to the army. The unit for would-be priests' training was located in Bartoszyce, near the Soviet Union border. Evidently, not being a coincidence, but another element of persecution of the Roman Catholic Church by the Communist regime. At this time military service was a greater opportunity for indoctrination of young men, especially harsh for seminarians, who underwent extra-intensive ideological "treatment". It was a great test of character.
Alfons Popiełuszko began his military service in the autumn of 1966. Persecution for religious practice was part of everyday life, with severe penalties for violation of prohibitions, even within the terms of military procedures. For example, traditional collective responsibility for any signs of "clericalism", such as possession of a rosary or a medal of Our Lady, was rigorously applied. Popiełuszko, the seminarian, survived this "school of life" intact. His strength of spirit overcame mindless violence as well as the imposed atheism. Although, after the military service the future priest suffered health problems (relating to heart and thyroid), this failed to stifle his calling and he returned to the seminary.