Mary Lee passed away in her sleep at age 80 and was remembered with a Scientology service.
TMZ reports Lee was battling a long illness before her death.
Cruise and his three sisters were at her service held this weekend at her local Church of Scientology, according to People.
Also at the service were several close friends and family members.
Mary Lee was last seen in Clearwater, Florida in May 2016 using a walker. She also appeared to have oxygen tubes attached to her.
Before that, she had not been seen since 2010.
Mary split from Tom's father, Thomas Cruise Mapother III, in 1974.
She went on to move to New Jersey and marry John 'Jack' South in 1978 when Tom was 16.
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