Late in 2003, Fanning appeared in Because of Winn-Dixie in the small role of Sweetie Pie Thomas. In 2004, she did voice work in the English-dubbed version of Miyazaki's animated film My Neighbor Totoro, in the role of Mei, opposite Dakota, who voiced Satsuki, the older sister to Elle's character. Later that same year, she filmed I Want Someone to Eat Cheese With. In early 2005, Fanning filmed scenes in Charlotte's Web as the "future granddaughter" of Fern Arable played by Dakota. However, the scenes did not make the final cut. In mid-2005, she played Debbie, the daughter of Richard and Susan Jones (played by Brad Pitt and Cate Blanchett) in the film Babel. In early 2006, Fanning filmed scenes in both The Nines and Déjà Vu. In mid-2006, she filmed The Lost Room, a science-fiction TV miniseries. Also in 2006, she appeared on the episode "Need to Know" of House: MD, playing the patient's daughter. She appeared in an episode of Criminal Minds in 2006, playing the supporting role of Tracey in "The Boogeyman".