Maxine Carr has admitted lying for Ian Huntley, but said she believed he was innocent and wanted to protect him.
Maxine Carr has appeared in the Old Bailey for the first time
Taking the stand at the Old Bailey for the first time, she said it had not crossed her mind Mr Huntley had killed Holly Wells and Jessica Chapman.
If it had, she would have told police "like a shot", the 26-year-old added.
Ms Carr denies helping an offender and conspiring to pervert the course of justice. Mr Huntley denies murder but admits conspiring to pervert justice.
Ms Carr took the stand after Mr Huntley spent the morning being cross-examined by the prosecution.
Her counsel, Michael Hubbard QC, said Ms Carr admitted telling police lies for almost two weeks after the girls disappeared.
AN EXCHANGE BETWEEN MICHAEL HUBBARD QC, DEFENDING, AND MAXINE CARR
Hubbard: We know you lied
Hubbard: To the police
Hubbard: To journalists
Hubbard: On television
Hubbard: And you lied right up until you were arrested
The jury must decide whether she did this deliberately, knowing or believing that he had killed the girls, he said - or because she believed he was innocent and wanted to protect him.
Speaking in a loud and clear voice, Ms Carr said she had been away in Grimsby the weekend Holly and Jessica disappeared.
Mr Huntley had told her on the phone the girls had been in their house after one of them had had a nosebleed, but had later left, she said.
On her return to Soham, she had noticed Mr Huntley's car had been cleaned and the carpet changed, but said Mr Huntley had told her he had had to clean it because their dog had made a mess in it.
Inside the house, she said, quite a lot of cleaning had taken place - which was surprising because Mr Huntley was not usually "domesticated".
She said Mr Huntley had seemed agitated: "He just wouldn't sit still. He was pacing up and down."
He had told her he was concerned he was going to be "fitted up", she said - because of a previous allegation of rape against him, which she had already known about.
"He said: ''Oh God, I'm the last person to have seen them, I'm going to be a suspect for this, they're going to be after me for this'."
EXCHANGE BETWEEN MICHAEL HUBBARD, DEFENDING, AND MAXINE CARR
Hubbard: It is suggested that you either knew or
believed Ian had killed those children
Hubbard: Did it ever cross your mind?
Hubbard: If you had ever had an inkling he was responsible, tell
the jury what you would have done
Carr: I would have been out of that house like a shot straight to the
At that point, Mr Huntley had suggested she provide him with an alibi, by saying she was in the bath on Sunday afternoon, she said.
Ms Carr said she had had no suspicions about the girls because Mr Huntley had told her they had left the house, and she had believed him.
"They had gone, they weren't in the house. So now it was just
about stopping people spreading rumours about [Mr Huntley] having children in the
house... it was all
about Ian, his job, his reputation."
Ms Carr was asked if she had thought she was doing wrong by lying for Mr Huntley.
"I just knew Ian wouldn't have done anything like that," she said.
She said if it had crossed her mind that he had done so: "I would have been out of that house like a shot and straight to the police."
There were tearful scenes in the courtroom as Ms Carr recounted how fellow inmates at Holloway Prison had branded her "Myra Hindley MkII" and a "nonce" over her links with Ian Huntley after she was taken into custody last August.
Earlier, Ms Carr said she loved Mr Huntley "very, very much" and wanted to have children with him.
She said she had also loved her temporary job as a teaching assistant at Holly and Jessica's school, and had been disappointed not to get a permanent position.
AN EXCHANGE BETWEEN RICHARD LATHAM QC, PROSECUTING, AND IAN HUNTLEY
Latham: You were actually praising the police?
Huntley: Yes, they was working hard
Latham: While you ran rings round them?
Huntley: I wouldn't say I was running rings round them
Latham: You were deliberately keeping one or two or three steps ahead
She said Holly and Jessica were "lovely", "bright" and "always laughing".
And she choked back tears as she described her time on remand in Holloway, where her fellow inmates called her "Myra Hindley Mark Two".
In the morning, Mr Huntley was cross-examined by prosecuting barrister Richard Latham QC, on his third and final day of giving evidence.
In a series of combative exchanges between the pair, the barrister accused Mr Huntley of "laughing" at police while sending them on false trails - which Mr Huntley denied.
Mr Latham also pressed Mr Huntley on his version of how the girls died.
Huntley insisted Holly died accidentally after falling into his bath, and denied killing Jessica "quite deliberately" because of what had happened to Holly.
The case was adjourned until Thursday.