[3][4] When they realized that the group would not return to the Philippines though there were many remaining who needed surgery, they established Operation Smile, Bill Magee said,[3] It was guilt ... We saw hundreds of children and saw many more turned away.

After establishing headquarters in Norfolk, VA, Operation Smile began foundations in Australia, UK, Italy, Vietnam, and Ireland.

[5] For each mission, Operation Smile verifies the credentials and organizes the participation and travel arrangements for a team of volunteers.

[6] The team typically includes a mission site coordinator, plastic surgeons, anesthesiologists, a pediatrician, an intensive care physician, head or coordinating nurse, pre- and post-op nurses, child development specialists, speech pathologists,[7] dentists and/or orthodontists.

[10] In November 1999, specific patient deaths[11] brought criticism on Operation Smile's medical procedures.

[12][13] In response, Operation Smile conducted an internal review, whereupon the organization publicly acknowledged organizational flaws.