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Miners had been drilling day and night to reach the boy, Julen, into the borehole - 100 metres (300 feet) deep and just 25 cm (10 inches) wide - which was blocked with soil.
"At 1:25 a.m. (0025 GMT), the rescue teams reached the area of the well where they were looking for Julen and they found the lifeless body of the little one," said a government spokesperson in Malaga.
There had been no signs of life since the boy had fallen into the borehole as his family was walking through a private estate in Totalan in southern Spain. Rescuers found the well was blocked with soil, raising fears the well had collapsed on top the child.