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Emergency services said the crash happened at about 7.45pm local time, roughly 360km south of Madrid.
A total of 122 people were reported injured, with 48 still in hospital and 12 in intensive care.
Spanish rail operator Renfe said around 400 passengers were travelling on the two trains involved, an Iryo service heading from Málaga to Madrid and an Alvia train bound for Huelva.
Spanish media reported the Huelva-bound train was travelling at around 200km/h at the moment of impact.
Images from the scene showed overturned, mangled carriages under floodlights as rescue crews worked through the night.
Transport Minister Óscar Puente said the death toll had reached 39 and could rise, praising rescue teams and offering condolences to victims’ families as he travelled to Córdoba.
Rail traffic between Madrid and Andalucía was heavily disrupted, with Spanish broadcaster RTVE reporting more than 200 services cancelled on Monday, affecting routes to cities including Córdoba, Seville and Granada.
Prime Minister Pedro Sánchez cleared his diary to respond to the incident, while investigators began examining what caused the derailment.
Spain has one of the world’s largest high-speed rail networks, and the crash revived scrutiny of the system after recent disruption from power problems and cable thefts.
The country opened parts of the network to private operators in 2020; Iryo began running services in 2022 as a joint venture involving Italy’s state railway group, Air Nostrum and Globalvia.
Reuters