Lee fed her through a tube, amazed at the child's hunger to survive. Hannah lived six more years: "When she died, I cried so much, more than even when my own parents passed away."
That's when Lee vowed he would never turn away a challenged child. He has officially adopted several as his own and gained temporary legal guardianship of others.
In 2009, he installed the drop box. Immediately, the babies began appearing, some with their umbilical cords still attached.
The child welfare people visited Lee in spring. They had seen a TV report on his orphanage. The drop box had to go.
Child abandonment is a crime in South Korea and they said Lee provided parents an easy out. They said the orphans also deserved to know the identity of their biological parents eventually, a service Lee could not provide with the anonymous drop-offs.
Although they acknowledge Lee is well-meaning, officials believe he may be doing more harm than good. "Just accepting an infant without going through the proper verification steps is wrong," said Lee Woon-gyu, a child welfare officer.
Social workers who recently visited the orphanage say that 21 children are far too many for a four-bedroom home; some called the conditions unsanitary. They added that the law requires a doctor to be on hand round the clock in case of an emergency.
Pastor Lee insists that his orphanage has been running safely and efficiently, but acknowledges that he wants to raise the money to build a larger facility. He says the drop box offers salvation for babies who might otherwise be deserted in trash cans or public restrooms. He refused to remove the box, but agreed to turn over any children left there. Since February, eight infants have been placed there.
On a recent day, he hurried around the orphanage, kissing each baby on the cheek and forehead as four donated washing machines hummed in the background.
The walls are covered with pictures of his brood, some of whom are named for the time they appeared in the drop box, such as Midnight and Autumn. Of the 32 children he has taken in, three have died, three went back to live with their parents, and five were adopted.
Lee says he loves them all equally, but there's one he cannot forget. Little Hannah is buried under a tree just outside Lee's front door. "I just couldn't let her go," he said. "It comforts me to know she's still here."
Jung-yoon Choi of The Times' Seoul bureau contributed to this report.