Two hundred Alexion employees returned to New Haven Tuesday after the company’s 16-year stint in nearby Cheshire, Connecticut.

These 200 were the first of the 1,000 employees Alexion plans to move to its 100 College St. headquarters by the end of March. Alexion, a pharmaceutical company founded in Science Park in 1992 that specializes in the treatment of rare disorders, moved to Cheshire in 2000 after struggling to find lab space in New Haven. But in 2012, the company announced that it would move back to the Elm City, bringing its resources closer to New Haven’s critical mass of scientists, biotech and collaborative research opportunities.

“As Alexion works to fulfill its mission to transform the lives of patients with severe and devastating rare disorders, the move to New Haven enables us to keep pace with the rapid growth of the company’s global operations and expanding pipeline initiatives,” Alexion Associate Director of Corporate Communications Emily Vlasek said.

Community Foundation for Greater New Haven President Will Ginsberg, a New Haven resident for more than 30 years, including four working as the city’s economic development administrator, said he has never seen a company as profitable and global as Alexion choose New Haven as its base. Alexion’s public shares are worth roughly $36 billion. He added that Alexion’s move is one of the most significant economic development victories in the city’s history.

The first day of operations at Alexion’s new headquarters — a 14-story glass complex housing 426,000 square feet of laboratory and office space — also marked the beginning of Here in New Haven, Alexion’s 30-day commitment to philanthropy in the city. Alexion plans to give daily grants of $1,000 to various New Haven charities through the CFGNH until Feb. 19, World Rare Disease Day. Columbus House and Arte Inc., a nonprofit that promotes Latino art, received grants on Tuesday and Wednesday, respectively.

Claire Criscuolo, owner of Claire’s Corner Copia, expressed her delight at Alexion’s homecoming, citing both the corporation’s lifesaving work and the customers the move will bring to local business.

“This company will bring more than a thousand people to our city, and we already have fed many of them in the past at events on their former campus,” Criscuolo said. “We look forward to feeding them many, many more times in the future, and getting to know them and share our beautiful city with them.”

Criscuolo added that she anticipates Alexion’s employees will enjoy their easy access to New Haven’s museums, performing arts venues, food and shopping facilities.

Alexion has strong ties to Yale as well as to the Elm City. It was co-founded in 1992 by professor of medicine and pathology Leonard Bell, who served as its CEO until last March.

Bell, who has since left his position at Yale, continues to serve as the chairperson of Alexion’s board and as a consultant to the company.

But Joseph Schlessinger, head of pharmacology at the Yale School of Medicine, said Alexion’s recent relocation will not drastically affect the University community.

“While it is nice to have more people interested in biomedical research in New Haven, I do not think that the relocation of Alexion to New Haven will have any impact on Yale or Yale’s Department of Pharmacology,” he said.

Schlessinger acknowledged, however, that many graduates of the Yale pharmacology program seek employment and are hired by pharmaceutical companies such as Alexion and by small biotechnology companies, some of which were founded by members of the Yale faculty.

Alexion’s trademark drug, Soliris, treats a rare genetic immunological disease called atypical hemolytic uremic syndrome.