The not-guilty plea for Kenneth Kyle, 46, of San Francisco, was entered by his defense lawyer, David Bigeleisen, at an arraignment in the court of U.S. Magistrate Bernard Zimmerman.
Dressed in red Alameda County jail clothing, Kyle said nothing during the brief court appearance. He agreed last month to waive a detention hearing and is being held without bail.
He is due to return to court April 29 for a status conference before U.S. District Judge Jeffrey White, the trial judge assigned to the case.
Kyle, an assistant professor of public affairs at California State University, is separately charged in Missouri with raping a 1-year-old girl and producing child pornography in that state.
He was indicted on the five federal counts on April 1. The charge of crossing a state line for purposes of aggravated sexual abuse of a child carries a mandatory minimum sentence of 30 years in prison and a maximum of life in prison if he is convicted.
The other charges in the indictment are producing, transporting, distributing and possessing child pornography.
The indictment alleges that the child sexual abuse and pornography production occurred between August and October 2009.
The alleged victim's mother, Tessa Van Vlerah, 20, of Ballwin in St. Louis County, Mo., is charged in the federal indictment with one count of producing child pornography depicting her own daughter.
Van Vlerah is in custody in St. Louis County on $2 million bail.
Both Kyle and Van Vlerah face two sets of charges in Missouri. In St. Louis County, they are accused of four Missouri state counts of raping Van Vlerah's daughter, sodomy, promoting child pornography and committing or promoting incest.
They were also indicted by a federal grand jury in St. Louis on March 31 on one count of producing child pornography between March 1 and March 15, 2010.
The two federal indictments differ in that the charges in the San Francisco indictment refer to dates in 2009, while the St. Louis indictment alleges pornography production in March of this year.