He was remanded in custody to a date yet to be fixed. He did not apply for bail during the landmark hearing on Monday, but said he preferred to be tried in Sierra Leone.
"Most definitely, I'm not guilty," Taylor told Judge Richard Lussick at the UN-backed Special Court for Sierra Leone.
"Most definitely, I did not and could not have committed these acts against the sister republic of Sierra Leone."
Krystal Thompson, the court's manager, read out the 11-count indictment against Taylor related to murder, sexual slavery, use of child soldiers and mutilation.
It was Taylor's first court appearance and a landmark one making him the first former African president to answer charges of crimes against humanity.
Taylor said: "I think this is an attempt to continue to divide and rule the people of Liberia and Sierra Leone."
Taylor questioned the jurisdiction of the court but later said he preferred the trial to take place in Sierra Leone. The Special Court has sought to have the trial moved to The Hague due to security concerns.
He said: "I do not recognise the jurisdiction of this court... its right to exercise jurisdiction over me as the 21st president of the republic of Liberia."
Taylor was last month reportedly in favour of facing trial in The Hague. His victims said they would like to see him tried here "to face the bitterness of the war" in Sierra Leone.
If convicted Taylor faces a lengthy prison term, but there is no death penalty, according to court officials.
The actual trial is not expected to begin for months at least, as the court has said it wants the proceedings moved to The Hague. It has also cited lack of adequate space this year at the courthouse in Freetown.