The archbishop of Chicago, Cardinal Francis George, led a graveside prayer service during the burials at Mt. Olivet Catholic Cemetery.
"Catholic Cemeteries have been part of this community since the beginning and we bury the dead because it's a corporal act of mercy," Cardinal George said.
Eighteen hearses pulled up to lay 13 adults and 120 unborn children to rest -- people with names but no family to bury them. Plywood boxes were transported to each plot.
Religious leaders expressed their concerns in January with operations at the Cook County Medical Examiner's Office. They called for changes to "ensure the dignified handling of the dead."
Officials said in January that coolers at the morgue meant to house 300 bodies had at one point held 363. County board President Toni Preckwinkle later announced an overhaul of the morgue.
Catholic Cemeteries offered to help bury the 300 bodies that were backlogged at the Cook County Medical Examiner's office.
The county says there is more work to do.
"We don't have it completely fixed now," said Cook County Sheriff Tom Dart. "Through the kindness of the Catholic Cemeteries, we're taking care of some of it now. But we are trying to make sure it's taken care of so we don't have to ever hear a story about this again," said Cook County Sheriff Tom Dart.
Dart's office has proposed a plan to have jail inmates build caskets.
Preckwinkle has created new positions at the morgue so a backlog never happens again.
"We've seen a considerable reduction in the number of remains in our care and custody," she said.
Wednesday's burial was about giving dignity to people that deserved more. Funeral directors that volunteered their services stood by each plot with a single flower on top of the caskets as the cardinal prayed.
"My dear friends, we gather today to lay our brothers and sisters to rest," Cardinal George.
The Associated Press contributed to this report