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Charles River was founded in 1947 by Henry Foster, a young veterinarian who purchased one thousand rat cages from a Virginia farm and set up a one-person laboratory in Boston overlooking the Charles River. He supplied local researchers with laboratory animals.
In 1955, the company's headquarters were relocated to their current home in Wilmington, Massachusetts. The organization became an international entity in 1966 by opening a new animal production facility in France.
The first commercial, comprehensive genetic monitoring program was implemented by Charles River in 1981. Three years later, they were acquired by Bausch & Lomb. In 1988, the organization began creating transgenic mice and rats. In the 1990s, they began in vitro endotoxin testing. In the 1990s, Jim Foster bought Charles River back from Bausch & Lomb, and the company later went public on the New York Stock Exchange.
Charles River launched the Humane Care Imperative in 2002, designed to raise awareness and train employees on animal welfare's importance. The same year, they were named "Company of the Year" by The Boston Globe. The company introduced preconditioning services in 2005 to provide customers with study-ready animals.
In 2008, Charles River signed a ten-year contract to partner with the National Cancer Institute and opened a facility in Frederick, Maryland.
In April 2019, Charles River announced it would cease its San Diego operations, moving the breeding of rodents for testing compounds to Hollister, California.
In March 2023, the Born Free USA animal welfare organization protested against Charles River's plan to export 1,000 endangered juvenile long-tail macaques to Cambodia for testing.