An Alberta couple who treated their son's illness with natural remedies rather than take him to a doctor have been found not guilty in the toddler's death after a retrial.

David and Collet Stephan were tried on charges of failing to provide the necessaries of life to 19-month-old Ezekiel, who died in 2012.

Supporters in the courtroom cheered and Collet Stephan cried as she hugged her husband.

Court of Queen's Bench Justice Terry Clackson spoke to the court in Lethbridge, Alta., for only four minutes on Thursday before releasing his written decision in the judge-alone trial.

The judge ultimately sided with the defence's medical experts in finding the boy had viral not bacterial meningitis and ultimately died of a lack of oxygen.

Speaking with the media after the decision was handed down, David Stephan called the last seven years an "emotional roller-coaster."

David Stephan speaking now <a href="https://t.co/hqj1lniX2l">pic.twitter.com/hqj1lniX2l</a> —@CBCMeg

"We didn't know what to expect coming into today, and it's the right decision, and it's shocking because it's been seven years of our life fighting this so it's become part of our identity," he said.

"It's a beautiful thought that we can move on with our lives."

Stephan said his case "helps protect parental rights" so that parents won't be held criminally liable if they choose alternative treatments for their sick children.

He also says the fight isn't over between his family and the Alberta government — he still wants to recoup the $1.2 million he says his family has spent in legal fees.

This was the second trial for the Stephans, who were found guilty by a Lethbridge jury in 2016. While the Alberta Court of Appeal upheld the conviction, the Supreme Court of Canada ruled the original trial judge erred in his instructions to the jury.

Stephan talks outside the Lethbridge courthouse on Thursday. He said the last seven years have been an 'emotional roller-coaster.' (Vincent Bonnay/Radio-Canada/CBC)

Appeal not ruled out

Back then, the official cause of death was bacterial meningitis.

However, in his written decision, Clackson wrote that he accepted the opinion of Alberta's former chief medical officer, Dr. Anny Sauvageau, who told court she does not believe Ezekiel actually died from bacterial meningitis.

"In this case, we know there is no specific treatment that is effective for viral meningitis," Clackson wrote.

"It follows that the Crown did not prove medical attention would have saved [Ezekiel's] life or that if he had viral meningitis and it was life-threatening [which is not established in the evidence], medical attention even could have saved his life."

In a written statement, the Alberta Crown Prosecution Service said it has not yet decided whether to appeal Clackson's decision.

"We respect the decision of the Court," reads the statement. "This has been a challenging case for everyone involved. The Alberta Crown Prosecution Service will review the decision to determine next steps."

Treated with natural remedies

Over the course of the trial, the Stephans testified that they initially thought Ezekiel had croup, an upper airway infection, and they treated him with natural remedies including a smoothie with garlic, onion and horseradish.

They said he appeared to be recovering at times, and they saw no reason to take him to hospital, despite his having a fever and lacking energy.

They called an ambulance when the boy stopped breathing.

David Stephan, who was representing himself, said in his final arguments that it was paramedics who caused Ezekiel's death by improperly intubating the boy.

Sauvageau also suggested Ezekiel might have lived had the first ambulance to Cardston, Alta., been better equipped to treat a child his age with breathing difficulties.

Clackson also heard evidence the parents suspected the boy had meningitis and were told days before he stopped breathing to take Ezekiel to a hospital or doctor.

"It's the Stephans' failure to respond to … increasingly alarming information or feedback from their child during that period of time," Crown prosecutor Britta Kristensen said in her closing argument.

"Both parents knew the child had meningitis."