Allan Young, 36, allegedly shook his baby son Michael so hard in the crib that he was left with brain damage, severe cerebral palsy, blind, and with a twisted spine that eventually killed him.
However, Mr Young, of Wishaw, North Lanarkshire, told the Old Bailey he could not be responsible for the injuries as he did not shake Michael that hard.
He told the jury: "I know how I shook him, and I didn't shake him that much, not with the excessive force that's been explained."
Asked whether he caused Michael's injuries, Mr Young replied: "I still don't know."
Michael had the mental age of a six-week-old baby when he died aged 12.
He was incontinent and had to be fed through a tube by his adopted mother.
His spine was so deformed that, as he grew older, it crushed his organs until he stopped breathing on January 23, 2011.
In a landmark case, Mr Young, who had already served a year in prison for attacking his son, was charged with manslaughter and is now back on trial.
Mr Young admitted shaking Michael in the early hours of April 16, 1998, when the baby would not stop crying.
He said he pleaded guilty to the attack on the advice of his solicitors, but could not remember seeing any medical evidence at the time.
Mr Young tearfully told the court how, the day after the attack, he and then-partner Erica Francis initially believed Michael had the flu.
He said: "At the time I didn't realise he was actually getting worse, but now I see it that he was getting worse."
He said the next morning Michael was "like a floppy doll - he was very poorly".
The accused said he confessed to shaking his son only after doctors had asked if Michael had suffered a fall or had been shaken.
"I can't put into words how it felt," he told the court, but denied demonstrating the shaking incident on a toy doll to Ms Francis prior to going to hospital.
Mr Young said he saw his son one last time in Great Ormond Street Hospital while on bail, but never saw him again after that.
He and Ms Francis were living in Kilburn, London, at the time of the incident, which happened between on April 16, 1998.
It is alleged Michael had suffered the devastating injuries that morning, but was not taken to hospital until the following day.
Mr Young is on trial for manslaughter as the prosecution claims the injuries he inflicted were directly responsible for the death.
The accused, who denies the charge, said he went into hiding after his release from prison, spending two years holed up in his bedroom fearing reprisals.
He said: "My life was at serious threat when I went back home, so I spent the first two years in my bedroom. I spent two years in hiding - how would anyone feel in that situation? I was deeply depressed and felt suicidal."
Mr Young said he eventually rebuilt his life with a new partner and they have a young daughter together in Scotland.
However, he said he remains on anti-depressants and quit his job when arrested against in 2011.
He has moved out of their home to avoid his partner and child being targeted. He said: "It is a very small community we live in and people do nasty things to your house because of the nature of the charges."
The trial continues.