Little Luca Monsellato was taken to hospital with a high fever and cold. He later died.
His parents, Marcello and Giovanna, had been giving the youngster fennel tea to treat his apparent cold, instead of other medical treatment.
They took him to hospital when it got worse, where hospital staff described him as looking 'pale, thin and breathless'.
Mr Monsellato, from Tricase in Italy, is a doctor of alternative medicine, an expert on acupuncture and is honorary president of Italy's Homeopathic Sinergy Association.
The couple have been bailed and deny any wrongdoing. Their lawyer, Alfredo Cardigliano, says they are thinking of bringing negligent charges against doctors at the hospital for not looking after Luca properly.
An autopsy found Luca died from natural causes, but police are still investigating his parents' actions.
Prosecutor Alberto Santacatterina said: "A manslaughter investigation has been opened against the parents of little Luca. We are looking into the events that surrounded his death and whether they were responsible by not giving him proper medical treatment when he was ill."
While Italy's Bioethics Committee said in a statement, ''medical practices that were not scientifically based could not substitute those that were scientifically proven," Fausto Panni from the association Omeoimpresse, which oversees the supply of homeopathic remedies said: ''The latest statistics show that during the last five years just 21 people have had side effects from homeopathic medicine with no fatalities.
''That compares to many who have died as a result of medical malpractice or adverse reactions to medicine.''
What a tragic story.
Do you use alternative medicines and therapies in your family?
Would you ever use them in replace of proper medical advice and treatment?