Herman Thomas, 48, denies the charges, which include sodomy, kidnapping, extortion, sex abuse and assault.
Up to 15 current and former prisoners are set to testify against him at the jury trial.
He was once the Democratic Party's choice to be the first black federal judge in south Alabama.
Mr Thomas resigned as a judge in 2007 following allegations that he spanked inmates in his private office at the county courthouse with a paddle. More...