Brandon Miller entered denials to the charges in Cuyahoga County Juvenile Court.
Denials are the equivalent of innocent pleas in adult court.
He was arrested Monday in the death of Diamond Miller, who died at a hospital a day earlier. Coroner Elizabeth Balraj said the infant died from massive head injuries and internal bleeding. The boy said he noticed the baby was not breathing and woke up the mother, who called 911. Miller was charged in Juvenile Court because state law requires that a person must be at least 14 when a crime is committed to be tried as an adult.