Speaking on the Pat Kenny programme on Radio One, Louise Mullen said her son's gold medal had not been "tarnished" by recent developments and instead proclaimed his innocence.
She also queried the identity of those behind the break-in at the headquarters of the Equestrian Federation of Ireland.
At times laughing and at other times clearly emotional, she said the family had been going through a difficult time since the A sample taken from Waterford Crystal tested positive for banned substances.
"Anybody who knows Cian and our family knows that he is totally innocent," she said.
"You have no idea what my family and my parents have been going through it's been dreadful.
"There was nothing untoward here, there was nothing going wrong."
She made her comments as senior figures in horse-racing circles in Ireland called for a public inquiry into the missing B sample, and as it was reported the substances found in Waterford Crystal were for use on humans and not horses.
"It was Hallowe'en the other evening and we had our pumpkins and our trick or treaters at the door, but who the hell broke into Goffs, that's what I want to know?" she asked.
She also joked she had purchased a computer and was going to write a book based on the saga.