Preliminary tests indicate the worker was infected with a strain which matched the one being worked on in the lab.
They are now well and back at CDC and no other staff were exposed.
Salmonella infections are usually acquired by eating contaminated food.
CDC said the worker was following standard protocols to perform a basic procedure on a frozen sample to culture or grow the bacteria.
The agency is investigating to see if additional safeguards are needed to prevent exposures when doing this in the future.
CDC said laboratory science is critical to protect America's health but it does carry risk.
“CDC has implemented numerous steps over the past few years to enhance its laboratory safety program, including standing up the Office of the Associate Director for Laboratory Science and Safety, reviewing laboratory safety protocols, and establishing the Laboratory Leadership Service fellowship program.”