Renowned for vivid paintings of bison and animal-headed humans, the rocky cave closed in 2002 because scientists said the breath from crowds of visitors was damaging the prehistoric paint.
Now it reopens to small, select groups of visitors who will have to wear masks and overalls while experts assess the impact on the paintings, the culture ministry said.
A highlight is a set of 14,000-year-old paintings of red and yellow bison plus horses, deer, humans with the heads of animals and mysterious symbols.
The cave, whose walls are covered with paintings over more than 270 metres (yards), was discovered in 1868 at Santillana del Mar, in the Cantabria region.
Experts say the cave was inhabited approximately 35,000 to 13,000 years ago.
The paintings are "exceptional testimonies to a cultural tradition and... Outstanding illustrations of a significant stage in human history", UNESCO says in its listing.
The techniques of the paintings and realistic animal details mark "one of the key moments of the history of art", it says.
In January, the foundation which manages the cave said it could reopen but only to groups of five people a week, and for just 37 minutes at a time.
The culture ministry said a first group of five, selected at random from visitors to a nearby museum, would be allowed into the cave today.
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