Sources tell The Hartford Courant detectives served a search warrant at the home of her estranged husband, Fotis Dulos early Saturday morning.
There were taking DNA samples.
Police were also spotted leaving Fotis' Farmington Connecticut mansion Friday evening.
On Friday, police expanded the search to Hartford, where police searched storm drains and K9s searched dumpsters.
Investigators are also searching a family home in Pound Ridge, New York, as well as Jennifer's rental home in New Canaan.
Dulos vanished May 24 after dropping off her five children at school.
The children, ages 6 through 11, are now staying with Jennifer's mother in New York City, under the watch of an armed guard.
Family members said the children are safe and doing well under the circumstances.
Jennifer and Fotis have been engaged in a bitter two-year custody battle.
In court documents, Jennifer alleged Fotis "exhibited irrational, unsafe, bullying, threatening and controlling behavior" and that he threatened "to kidnap the children" and take them out of the country.
Fotis disputes the accusations, and fired back says she is "incapable of parenting" because of her use of mental health medications.