Castro kept dropping his head and closing his eyes during his court appearance, The (Cleveland) Plain Dealer reported.
Common Pleas Judge Pamela Barker ordered him several times to raise his head, saying she wanted to make sure he understood what was going on.
"I'm trying," he said after one of Barker's admonitions.
The indictment handed up last week incorporates some previous charges in a 329-count indictment. It covers the entire span of the women's alleged captivity, including 446 charges of rape and 512 of kidnapping, as well as three counts of child endangerment.
Castro allegedly fathered a child with one of his victims. He faces a charge of aggravated murder for allegedly inducing a miscarriage in another woman by repeatedly punching her.
His lawyers have said Castro would be open to plea negotiations if prosecutors do not seek the death penalty.
Amanda Berry, Gina DeJesus and Michelle Knight were freed after one of the women escaped and sought help from a neighbor.