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Farley, an infectious disease specialist and department chairman from Tulane University in New Orleans, will replace Dr. Thomas Frieden on June 8.

"My goal as New York City Health Commissioner would be to continue to make advances against the leading causes of death in New Yorkers today, such as smoking and obesity, while also constantly improving the ways we carry out our traditional mission, such as protecting residents from the threats of infectious diseases like influenza," said Farley.

A New Jersey native, Farley served as a senior adviser to Frieden from 2007 to 2008. The two have paired up on an article detailing the city Department of Health's initiatives, such as banning trans fats and requiring calorie count information in restaurants.

The mayor said Farley is a great choice to continue Frieden's work.

"He is a dynamic leader who time and time again shown himself up to any challenge," said Bloomberg. "New York City has always been a pacesetter, as you know, in the realm of public health, and with his passion for innovation and cutting edge public health policy, I am confident that Dr. Farley will pick up the pace even further."

Frieden was named by President Barack Obama to be the head of the Centers for Disease Control and Prevention.