The case, which has received significant media coverage since the baby's death in 2009, is exceptional because legal procedures against doctors are very rare in Sweden, where malpractice cases usually go before the National Board of Health and Welfare (Socialstyrelsen) with no criminal ramifications.
The case has raised concerns in medical circles, leaving doctors uncertain and wary of performing certain operations for fear of legal consequences.
The 57-year-old doctor, a woman whose name has not been disclosed, has been charged with manslaughter or alternatively attempted manslaughter for allegedly administering excessive doses of thiopental, an anaesthetic, to a very sick three-month-old baby that was born prematurely and was expected to die shortly of brain damage.
The doctor had removed the child from a life support system after consulting with the family and concluding that the baby's life could not be saved.
But an autopsy ordered by the family later found that the infant had received abnormally high doses of thiopental, and the family then had charges pressed against the doctor.
On Tuesday the doctor denied having administered thiopental and entered a plea of not guilty, her lawyer Björn Hurtig said, Swedish news agency TT reported.
She faces six to 10 years in prison if convicted.
Marta Christensen, the deputy head of Stockholm's Association of Medical Practitioners, said the case has left many doctors rattled.
"To question yourself is part of the job but now maybe they think things over a bit more and that means longer decision-making processes that in the end can unnecessarily delay medical care. A sense of insecurity has plagued the entire medical corps," Christensen told Swedish daily Svenska Dagbladet.
While the court has to determine whether or not the doctor administered thiopental, a top Swedish expert in penal law said in an editorial in newspaper of reference Dagens Nyheter that the prosecutor was wrong to press charges.
Professor emeritus Margareta Leijonhufvud argued that in end-of-life medical care, ethical guidelines allow doctors to administer painkillers even if it means death comes sooner than it otherwise would have.