His research has focused on experiments that trap and cool atoms to temperatures close to absolute zero,[1] and he led one of the first groups to realize Bose–Einstein condensation in these systems in 1995.

[2] For this achievement, as well as early fundamental studies of condensates, he was awarded the Nobel Prize in Physics in 2001, together with Eric Allin Cornell and Carl Wieman.

Ketterle serves on the board of trustees of the Center for Excellence in Education (CEE),[12] and participates in the Distinguished Lecture Series of CEE's flagship program for high-school students, the Research Science Institute (RSI), which Ketterle's own son Jonas attended in 2003.

Ketterle sits on the International Scientific Advisory Committee of Australia's ARC Centre of Excellence in Future Low-Energy Electronics Technologies.

[13] Ketterle is one of the 20 American recipients of the Nobel Prize in Physics to sign a letter addressed to President George W. Bush in May 2008, urging him to "reverse the damage done to basic science research in the Fiscal Year 2008 Omnibus Appropriations Bill" by requesting additional emergency funding for the Department of Energy's Office of Science, the National Science Foundation, and the National Institute of Standards and Technology.