If confirmed, he would be the fifth head of a massive department that was cobbled together from 22 agencies after the terrorist attacks of Sept. 11, 2001.
It now has an annual budget of $41 billion and 240,000 employees who are responsible for border security, immigration control, cybersecurity, screening passengers at airports and other tasks.
The sharpest questioning came from Sen. Kamala Harris, D-Calif., who was elected in November, over the future of the Deferred Action for Childhood Arrivals program.
DACA, as the program begun by President Barack Obama is known, defers deportations for hundreds of thousands of undocumented immigrants who arrived in the U.S. as children, grew up here and committed no crimes.
Harris pressed Kelly about whether he would use the DACA information to identify and deport people. She asked him to honor the Obama administration's promise not to use DACA applications to assist in deportations.
Kelly said convicted criminals and other categories of undocumented immigrants might be a higher priority for removal, though he acknowledged he had not had discussions with Trump's advisers about immigration policy.
"There's a big spectrum of people who need to be dealt with in terms of deportation," he said. "I would guess that (DACA applicants) might not be the highest priority" for deportations, Kelly said. He added, "I promise you that I will be involved in the discussion."
Kelly also seemed to raise questions about Trump's vow to use "extreme vetting" of refugees and immigrants to prevent Islamic militants from entering the country.
"You can't guarantee 100 percent, and if you are taking in large numbers of people from places where you really can't vet them very well you do the best you can," Kelly said.
A native of Boston, Kelly enlisted in the Marine Corps in 1970 after high school and became an officer after graduating from the Naval Academy.