The body of the unidentified toddler was found by railway workers who were weeding alongside train tracks in the village of La Argañosa in Spain's Asturias region.
An autopsy has now revealed signs of violence with blows to various parts of the body, with police now suspecting a violent death for the child, regional broadcaster RTPA reported on Tuesday.
Coroners in the regional capital of Oviedo have now sent DNA samples to the Madrid Institute of Toxicology to try and identify the child, and to ascertain if he was administered with tranquilizers or other toxic substances.
National police are continuing to investigate the cause of child's death.
Police sources said railway workers on Monday discovered the suitcase, which had been camouflaged by vegetation. When they touched the piece of luggage they discovered there was something inside wrapped in a blanket.
It was then they discovered the foot of the child, sources said.