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Pharmacia company was founded in 1911 in Stockholm, Sweden by pharmacist Gustav Felix Grönfeldt at the Elgen Pharmacy. The company is named after the Greek word φαρμακεία, transliterated pharmakeia, which means 'sorcery'. In the company's early days, much of its profits were derived from the "miracle medicine" Phospho-Energon.
During World War II, Swedish chemist Björn Ingelman (who worked for Arne Tiselius at Uppsala university) researched various uses for the polysaccharide dextran. Together with the medical researcher Anders Grönwall, he discovered that dextran could be used as a replacement for blood plasma in blood transfusions, for which there could be a large need in wartime. Pharmacia, which then was still a small company, was contacted in 1943 and its CEO Elis Göth was very interested. The product Macrodex, a dextran solution, was launched four years later.
Dextran-based products were to play a significant role in the further expansion of Pharmacia. In 1951, the company moved to Uppsala, Sweden, to get closer to the scientists with whom they cooperated, and Ingelman became its head of research. In 1959, Pharmacia pioneered gel filtration with its Sephadex products. These were also based on dextran and discoveries in Tiselius' department, this time by Jerker Porath and Per Flodin. In 1967 Pharmacia Fine Chemicals was established in Uppsala. In 1986 Pharmacia Fine Chemicals acquired LKB-produkter AB and changed name to Pharmacia Biotech. Pharmacia Biotech expanded their role in the 'biotech revolution' through its acquisition of PL Laboratories from Pabst Brewery offering a line of recombinant DNA specialty research chemicals. Sold to private interests in the 1990s, Pharmacia was first merged with "Kabi Vitrum" to form Kabi Pharmacia with headquarters in Uppsala. Kabi was later excluded. Then the company merged with the American pharmaceutical company Upjohn in 1995 and moved its headquarters to London.
In 1997 the Uppsala based biotechnology division Pharmacia Biotech merged with Amersham Life Science (U.K.) and took the name Amersham Pharmacia Biotech. The Pharmacia name was later dropped when Pharmacia & Upjohn sold its share of the company to Amersham plc. The company changed its name to Amersham Biosciences in 2001. In 2004 Amersham Biosciences was acquired by GE Healthcare. The Life sciences division of GE Healthcare still has its headquarters in Uppsala.
In 1999, the nutrition division was sold to Fresenius. The merged company "Pharmacia & Upjohn" merged with the American bioindustry and medical company Monsanto Company in December 1999 (Monsanto had acquired the pharma company G. D. Searle & Company in 1985).  The resulting conglomerate took the name of "Pharmacia Corp." Monsanto, via its Searle division, had developed celecoxib which became a blockbuster drug soon after its approval by the FDA at the end of 1998.
In July 2002, Pharmacia and Pfizer announced an agreement that Pfizer would purchase Pharmacia; control of celecoxib was often mentioned as a key reason for Pfizer's acquisition of Pharmacia.  The deal was finalized in April 2003.
In 2004, the Uppsala based allergy-diagnostic division of legacy Pharmacia was sold off as Pharmacia Diagnostics. On January 16, 2006, Pharmacia Diagnostics announced that its name was changed to Phadia, which has ended the use of the Pharmacia trademark. Later in 2004, the Uppsala-based ophtalmology division was sold to AMO. The remains of Pharmacia in Uppsala was sold to the Indian company Kemwell in 2006. The remains of the Stockholm based part of Pharmacia was partly spun off to Biovitrum in 2001, which sold off its plasma products division to Octapharma in 2002. The rest was moved to Belgium in 2008. The company's facilities in Strängnäs Sweden are presently being expanded for the production of Genotropin, a growth hormone.
Pharmacia was one of Uppsala's largest employers outside the public sector, with over 4000 employees in the Uppsala region in 1996. However, the biotechnological know-how remaining in the wake of Pharmacia, as well as the presence of biotechnology research and education at Uppsala University, led to a larger number of people being employed in the sector in 2005 compared to 2002 when the merger with Pfizer took place. Many small and medium spin-offs from Pharmacia have granted future employment to many.