Peterson entered his plea during a brief arraignment in Stanislaus County Superior Court in Modesto.
District Attorney James Brazelton said in his filing that Peterson, 30, acted "intentionally, deliberately and with premeditation" in killing 27-year-old Laci Peterson and Conner Peterson, the couple's unborn child.
In a press conference held Monday evening, Laci Peterson's family said they would not jeopardize court proceedings by commenting on Scott Peterson's possible involvement in her disappearance, then thanked those who helped search for their missing daughter.
In an emotional statement, Laci Peterson's mother, Sharon Rocha, tearfully recounted what she called a nightmarish few months.
"I love my daughter so much. I miss her every minute of every day," she said. "My heart aches for her and Connor... I literally get sick to my stomach when I allow myself to think about what may have happened to them. No parent should ever have to think about the way their child was murdered."
She also said the person responsible for Laci's death "should be held accountable and punished for the tragedy and devastation forced upon so many of us."
"I can only hope that the sound of Laci's voice, begging for her life, begging for the life of her unborn child, is heard over and over and over again in the mind of that person every day for the rest of his life," said Mrs. Rocha.
Laci Peterson's father, Dennis Rocha, broke into sobs as he thanked community members and local authorities for their efforts. "Now we can move forward," he said, "Now justice can be done."
The bodies of Laci Peterson and her unborn baby boy washed ashore last week about three miles from where Scott Peterson said he was fishing in San Francisco Bay when his wife vanished.
The charges against Peterson include the special circumstance that he committed more than one murder, allowing the district attorney to seek the death penalty. Brazelton said he would likely seek the death penalty.
"It's hard for me to realistically believe it is anything but a death penalty case at this time," he said.
Public defender Tim Bazar was assigned to the case after Peterson said he could not afford to hire a lawyer. The case was continued until a May 6 bail hearing.
Laci Peterson's parents and in-laws were in court for the hearing.
Before the arraignment, Jackie Peterson, Scott Peterson's mother, hugged the mother of Laci Peterson.
Scott Peterson was led into the courtroom in shackles and a red jail jumpsuit.
As Judge Nancy Ashley read the charges, Laci Peterson's mother, Sharon Rocha, wept.
Scott Peterson was arrested Friday in San Diego County because detectives feared he might try to flee the country and was order held without bail at the Stanislaus County jail.
When he was arrested, Peterson's naturally dark hair was reddish-blond, he had grown a goatee. He had $10,000 in cash with him in his car, said a law enforcement source who spoke on condition of anonymity.
Scott Peterson's attorney, Kirk McAllister, talked with him Saturday night but has made no public comment on the case.
CBS News Legal Analyst Andrew Cohen notes that even so, there are early indications on what may be a key part of the defense case.
"Things are rarely as simple at the outset of these cases as police and prosecutors say they are and already we are getting hints from the Peterson family about one of the defense themes we may see. Scott's parents are complaining that the police focused on their son to the exclusion of other possible suspects," says Cohen. "If the defense can give some examples of this, the case may be a closer call than most people think."
Scott Peterson's mother and his father have both said they are sure their son is not guilty.
"It's something I didn't want to see happen, I didn't anticipate," said Lee Peterson of his son's arrest.
"He could not do anything bad," said Peterson, commenting in an exclusive interview on the CBS News Early Show. "He and Laci were so much in love. I mean, they had just a wonderful relationship. They were just so happy and anticipating the baby."
Investigators had long declined to name Peterson as a suspect, but even before DNA tests identified the bodies, Modesto police arrested him Friday near San Diego because they feared he might flee to Mexico, according to Modesto Police Chief Roy Wasden.