Ekain Cave was discovered by two members of the Antxieta Club of Azpeitia, Andoni Albizuri and Rafael Rezabal, during a speleological and archaeological exploration. In fact, during the spring of 1969 they set out to survey the solid limestone area near Azpeitia called Izarraitz. They returned following the Goltzibar stream towards Zestoa; there the country house at Sastarrain and its surroundings caught their attention. They were struck by its position between the two streams, the abundance of water and the favourable conditions for prehistoric habitation.
On 1st June the two friends went to the mentioned country house to ask the lady of the house, if there were caves in the hills and the limestone slopes. She said that there were and she showed them where they were, more or less. On 8th June they returned with equipment suitable for examining and carrying out a trial dig of the small cave, which measured 13 metres long and 2 metres wide. While they were preparing to make the dig at the left side of the entrance, Rezabal noticed a small hole on the right side of the entrance where cold air was escaping from.
They removed enough lumps of stone from the small hole until there was enough space to crawl through. They slithered along the ground for about twenty metres until they could stand up. They explored the first passages and, after noticing pigment on the walls, Rezabal discovered the panel of horses (Zaldei). They were so overcome with emotion that they couldn't carry on surveying the cave, so they decided to leave.
That afternoon they informed of the discovery to Jose Miguel de Barandiaran, who had been directing archaeological excavations in the Basque Country since 1916, and to Jesus Altuna, Director of the Prehistory Department at the Aranzadi Science Society.
As the cave had no name, it was given the name of the hill Ekain. Three weeks later the two researchers began the first survey of the sanctuary, and the results were published at the end of 1969. At the same time, samples were taken from the vestibule of the cave. These samples proved positive, indicating the existence of a prehistoric site. The site was excavated between 1969 and 1975 during six different digs.