Harris - dressed in a blue suit, white shirt and red tie - appeared in London's Southwark Crown Court for a plea and case management hearing ahead of his trial scheduled for April 30.
The 83-year-old, appearing relaxed and much healthier than his last court appearance in September, answered with a load and clear "not guilty" as each of the indecent assault charges were read to him in the packed courtroom.
Harris also remains charged with making four indecent images of a child in 2012. He is yet to be arraigned on those charges.
Harris was accompanied to the court in central London by a group of around a dozen friends and family including his elderly wife Alwen, whom he pushed in a wheelchair, and his middle-aged daughter Bindi.
He sat still and appeared relaxed in the dock during the hearing, which lasted more than an hour, speaking only briefly to confirm his name and enter his pleas.
The court heard Harris is accused of 12 separate counts of sexual assault, involving four alleged victims.
He was last year charged with six counts of indecently assaulting a 15-year-old girl in 1980 and 1981 and three charges of indecently assaulting a girl aged 14 in 1986.
Last month he was charged with a further three offences; one against a 19-year-old in 1984, one against a girl "aged seven or eight in 1968 or 1969" and another against a 14-year-old in 1975.
The count relating to the 19-year-old involved the same alleged victim as six of the earlier counts.
Harris was also previously charged with four counts of making indecent images of a child in the first half of 2012.
Today was Harris' first appearance in court since a hearing at Westminster Magistrates' Court in September, when he looked frail and confused.
He is expected to attend at least two more hearings before his trial is scheduled to begin.
Justice Nigel Sweeney renewed Harris' bail conditions, which dictate that he does not contact prosecution witness and lives at his home address in Bray.
Harris made no comment to reporters after the hearing as he walked past a huge media scrum held behind barricades at the front of the court.
Harris was questioned under caution in November 2012 by officers working on Operation Yewtree, the national investigation launched after abuse claims were made against Jimmy Savile.
He was then arrested in March, and charged in August. The allegations against Harris have no connection to Savile.
Harris has not commented on the allegations since he was first named in the press in April.
Harris, who painted a portrait of the Queen in 2005 and performed at her Diamond Jubilee concert last year, has been in the public eye for decades.
He had his first musical hit Tie Me Kangaroo Down, Sport in 1960, and continued to enjoy success in the industry as well as forging a television career.
