First he worked as an assistant at the Medical University Clinic in Vienna for Franz Chvostek junior and afterwards for Hans Eppinger.

During the war, he performed human experimentation involving seawater on inmates at Dachau concentration camp.

In early 1947, the Vienna prosecution initiated proceedings against Beiglböck because of war crimes, mistreatment, and violating human rights.

The experts claimed no deaths or long-term damage had occurred among the test subjects, and that Beiglböck had acted with the best medical intentions.

During Beiglböck's funeral, a state physician representative said that "after the war he was caught up in a wheelwork of hatred that knew no justice."

"Today his research during the Nazi period is being continued in the U.S. A West German newspaper reported that while Beiglböck's "innocence was clearly proven by the statements of those involved and by scientific expert opinions, most recently by that of the highest professional body in the Federal Republic, the Deutschen Gesellschaft für innere Medizin, and Professor Beiglböck was fully rehabilitated, these matters were taken up again last year by trying to prevent a lecture before the Vienna Medical Chamber.

Professor Beiglböck suffered greatly from this defamation, since he saw Vienna as his home, not only as a human being but also as a scientist, to which he was thus denied access."

[citation needed]During a meeting in Wiesbaden in 1964, a DGIM official declared that "Wilhelm Beiglböck was a true student of Eppinger.

His brilliant rise at the Vienna Clinic was abruptly and undeservedly interrupted by the misfortune of his detachment to carry out the so-called seawater experiments.

It must be said again at this point that the review of these experiments by a commission of the Deutsche Gesellschaft für innere Medizin, chaired by Mr. Oehme, absolved him of any guilt.