On 13 February 1840, on the recommendation of Ludwig Freiherr von Türkheim, chairman of the Imperial Committee of Education, he was appointed to the unpaid position of chief physician of the department for tuberculosis just opened in the general hospital.

Škoda began his clinical studies in close connexion with pathological anatomy while assistant physician of the hospital, but his superiors failed to understand his course, and in 1837, by way of punishment, transferred him to the ward for the insane, as it was claimed that the patients were annoyed by his investigations, especially by the method of percussion.

österreichen Kaiserstaates, included: His small, but for many years afterwards, unsurpassed chief work, Abhandlung über die Perkussion und Auskultation (Vienna, 1839), was repeatedly published and translated into foreign languages and established his universal renown as a diagnostician.

In 1841, after a journey for research to Paris, he made a separate division in his department for skin diseases and thus gave the first impulse towards the reorganization of dermatology by Ferdinand von Hebra.

As a matter of fact his therapeutics were exceedingly simple in contrast to the great variety of remedial agents used at that time, which he regarded as useless, as in his experience many ailments were cured without medicines, merely by suitable medical supervision and proper diet.

His high sense of duty as a teacher, the large amount of work he performed as a physician, and the early appearance of heart disease are probably the reasons that from 1848 he published less and less.