In 1862 he was appointed second assistant to professor Carl Braun in the maternity clinic at Vienna General Hospital. He was encouraged by Braun to study airborne organisms as the source of childbed fever. As such, Mayrhofer was asked to support the position of Braun in his extremely bitter feud with Ignaz Semmelweis, who claimed that the disease was caused by contaminated hands, in effect blaming doctors for the horrific mortality rates at the time (i.e. that it was an iatrogenic disease). Mayrhofer referred to these organisms as vibrions. At first, Mayrhofer's work supported Braun's views and the results were published. In an 1865 publication, however, Mayrhofer concluded that infection was usually the result of contaminated hands thus rejecting Braun's concept and supporting Ignaz Semmelweis' rivalling theory. Openly disagreeing with his superior, his fate was sealed. Mayrhofer's work was rejected and he soon left the clinic. He entered into private practice. He was appointed privatdozent of obstetrics in 1870, and a few years later, adjunct professor within the same field.