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Pharmacy was one of the first scientific subjects taught at the National and Kapodistrian University of Athens. The "Theoretical and Practical branch of Surgery, Medicine and Pharmacy" was established in Athens on May 18th, 1835 by Royal Decree, exactly one year prior to the Royal Decree of 1836 which inaugurated the University of Athens.

It is remarkable that prior to the 1821 Revolution, there were no pharmacies in Greece except on the Ionian Islands. In 1822 one was opened in Nafplio by Theodore Paschalis, a pharmacist who had studied medicine at the University of Padua, Italy. In 1825, the Greeks of Trieste, responding to the serious shortage of pharmacies in Greece, sent one of their pharmacists, Bonifacio Bonafin, to establish the first organized pharmacy in Nafplio. By 1850, the number of pharmacies established in Greece, by Greeks who had studied in Athens or at the Ionian Academy of Corfu or abroad, numbered 80.
The Department of Pharmacy, as a self-contained Department of the Medical School, joined the "Hellenic University of Otto" in 1843. The first courses taught over 3 semesters were Physical Chemistry, Natural History, Medicine, Botany, Pharmacology, Toxicology and their related laboratory-based practical courses. Greek and Latin courses were also added and 3 years of practical experience in a pharmacy were required prior to obtaining a license to practice pharmacy. The duration of the curriculum was extended to 2 years.  

During the first two years of the University's operation, no students were enrolled in the Department of Pharmacy. However, during the third academic year (1839-1840), five students were enrolled, and they received their Pharmacy degree in May 1941.

In the past, the Department of Pharmacy, has been repeatedly subjected to amendments/modifications. In 1905, it became affiliated to the newly founded School of Physics and Mathematics until 1911, when it became a part of the School of Medicine until 1922, after which it became once again affiliated to the School of Physics and Mathematics as the Department of Pharmacy, until 1982, at which time it became a department of the School of Health Sciences along with Medicine, Dentistry and Nursing.

In 1990, the (No. 32/90) decision of the Council of State annulled the Presidential Decree No. 410/87 with which the School of Health Sciences was established, and the Department of Pharmacy became an independent department until January 9th, 2014 when the department was once again incorporated into the School of Health Sciences.

The first Royal Pharmaceutical Laboratory was located at the corner of Academias and Vassilis Sofia Streets in Athens. The first official laboratory of the University was founded in 1837 and housed in the residence of the architects Stamatios Kleanthis and Eduard Schaubert, on the north slope of the Acropolis, in Plaka (now the Museum of the University). 

In 1870, the first building of the “Chimeio” was built in the courtyard of the Papadopoulou house (on the corner of Massalias and Akadimias streets) and in 1928 it was transferred to the center of Athens (Solonos street). The “Chimeio” was originally built in 1890 but was destroyed by fire in 1910 and reopened in 1913. 

Since 1992, the Department of Pharmacy has been housed within the School of Sciences on the University Campus of the National and Kapodistrian University of Athens.  

The first Chair of Pharmacy founded was that of Pharmaceutical Chemistry, and in 1932 the Chair of Pharmacognosy was established. The Chair of Pharmaceutical Technology was established much later, in 1979. These chairs were renamed Sections pursuant to the 1268 Law of 1982.

The duration of the Pharmacy degree since the 1993-94 academic year is five years (10 semesters), in accordance with the Presidential Decree 110/1993.