Mark Goudeau entered his plea by way of closed circuit television from jail.
He's charged with 20 felony counts, most connected to a 2005 attack on two sisters. Authorities say the attacks are among 23 crimes — from murder to rape and robbery — that police have been looking into as part of the Baseline Killer investigation.
The case takes its name from a road defining the city's southern limits.
Goudeau hasn't been connected to the other attacks. But police say they have not ruled him out as a potential suspect.
Goudeau was arrested at a traffic stop near his home, reports Tammy Leitner of CBS affiliate KPHO-TV.
The man's wife, Wendy Carr, told The Associated Press that police had arrested the wrong man.
"My husband is innocent," Carr said in a telephone interview. "This is a huge miscarriage of justice. And they have an innocent man in prison. This is all a mistake. He shouldn't be in prison for something he didn't do."
"His arrest is a good thing," Mayor Phil Gordon said. "Any individual who has been arrested for rape and kidnapping is a violent monster off the street. That's a good day."
Goudeau's neighbors said that they couldn't believe he would attack anybody and that he didn't resemble the police sketch that has been widely circulated depicting the Baseline Killer as a man with dreadlocks.
They described him as friendly, a cement worker who left early in the morning for jobs around the county and was a regular presence in his front yard, where he'd keep meticulous care of his bushes and waved to neighbors.
The "Baseline Killer" has been linked to 23 crimes in the Phoenix metropolitan area dating to August 2005, including eight killings. The crimes also include 11 sexual assaults of women and young girls and several robberies. The earliest crimes occurred along Phoenix's Baseline Road, where the name "Baseline Killer" originated.