Police had a warrant for the house, but the reason for the search was unclear. FBI spokeswoman Bridget Patton said the search is not based on any sort of tip.
Authorities left with several bags filled with undisclosed items. No law enforcement officials would comment on the nature of the latest search.
Lisa Irwin has been missing since Oct. 4. Deborah Bradley, the mother of the 10-month-old, is under scrutiny after inconsistencies emerged in her story. She admitted she drank heavily that night and may have blacked out.
The family's lawyer, Joe Tacopina, said he didn't know about the warrant, adding that a warrant wasn't even needed.
"They can go in and out any time," Tacopina said. "They have had unfettered access because we want answers."
He said the family hasn't been back to the house in the past couple of days because they don't want to interfere with the investigation.
The Associated Press contributed to this report.