Greenburg has been married three times. His first wife was writer Nora Ephron; their marriage ended in divorce after six years. His second wife, from 1980-1998, was reporter Suzanne O'Malley, who wrote a series of articles on the Andrea Yates case, later resulting in her book, Are You There Alone: The Unspeakable Crime of Andrea Yates (2004). Before their divorce, Greenburg and O'Malley had a son, Zack O'Malley Greenburg, after whom his father named his best-selling series of children's books. Zack played the title role of Lorenzo in the film Lorenzo's Oil. Greenburg is currently married to Judith C. Wilson, who as J.C. Greenburg writes children's books.