Scientists using radar imaging equipment have discovered the ancient passageways at "Gilmerton Cove" extend much further than originally thought.
More chambers have also been uncovered during the research project, BBC Scotland has learned.
The caves lie under the former mining village of Gilmerton in the south of Edinburgh.
Druids and witchcraft
Experts have long been baffled by the origins of the underground passageways and chambers.
They include stone benches, tables and even a small chapel hand-carved out of the sandstone.
The network has been linked to druids, witchcraft, a gentlemen's drinking den and even Mary Queen of Scots.
Now scientists from the universities of St Andrews and Edinburgh are using ground-penetrating radar equipment to map out what else may lie beneath.
The waves bounce off cavities or tunnels carved into the rock below.
The team has discovered that the subterranean network is at least double the size originally thought.
Simon Shackley, from Edinburgh University's School of Geosciences, said: "On the other side of Gilmerton Road there is a rather large chamber that is probably about 4m [13ft] deep."
"There also appear to be cavities in front of the cove and behind it - both about 2m deep".
"Perhaps by the work we're doing - if we're getting a bigger picture we're mapping in a more extensive way the footprint of it - then what we're hoping is that will tell us something about the use," he said.
"If it's got lots more passageways or maybe it's only got these two single passageways, but they might be leading somewhere else. And where they're leading to could potentially tell us what these were used for."
The scientists are now putting together a proposal to undertake more detailed 3D imaging of the site to give them a better picture of the cave network.
Margaretanne Dugan, owner of Rosslyn Tours and a guide at Gilmerton Cove, said: "It's incredibly exciting. We would love it if we could finally find out what lies beyond the blocked tunnels, if we could unlock those secrets and solve the mystery once and for all."
By Fiona Stalker, BBC Scotland reporter
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Gilmerton Cove in Drum Street beat the city's castle, zoo and the National Museum of Scotland on a review website.
They reached number one on a list of Things To Do in Edinburgh. Tours of the network of tunnels and chambers opened 10 years ago.
Groups of just 12 visitors at a time are allowed in.
The origins of the hand carved tunnels, which are at least 300 years old, remain a mystery, with rumours of them being used as a drinking den for 18th Century gentry, a lair inhabited by Knights Templar or a refuge for Covenanters fleeing persecution.
Margaretanne Dugan, owner of Rosslyn Tours, which runs tours at Gilmerton Cove, said: "We only open if we have a booking but we're definitely seeing more and more interest, especially from overseas visitors.
"To be the top-rated attraction in Edinburgh is fantastic for such a wee place."
Gilmerton Cove consists of a 40ft corridor with rooms off either side, but Ms Dugan said there may be more tunnels yet to be uncovered.
She added: "All of the tunnels haven't even been explored as it is unsafe to do so."
Edinburgh City Council began to develop the site in 1998 after buying it for £1.
The attraction opened as a heritage centre after a £100,000 restoration project.
The 45-minute tour starts at a small mining cottage in Gilmerton, where visitors descend 16 steps to reach the chambers below.
The survey of attractions was run by the TripAdvisor review site.
Source: BBC News
Gilmerton Cove has become one of Edinburgh's most highly rated tourist attractions since it opened in 2003.
A network of secret underground tunnels have turned an Edinburgh suburb into the latest hotspot on the city's heritage tourist trail.
Gilmerton Cove has proved to be one of the most highly rated attractions since it reopened in 2003 following a five-year collaborative project between Gilmerton Heritage Trust and The City of Edinburgh Council.
Users of the website TripAdvisor have rated it more highly on average than Edinburgh Castle, the National Museum of Scotland and the city's zoo.
The caves have been inhabited for at least 300 years and various theories exist about what they were used for, among them that they may have been a meeting place for the Covenanters, who were persecuted in the 17th century for opposing the religious reforms of King Charles I.
Records show they were inhabited by George Paterson, a blacksmith, in the 18th century, but archaeologists say the network could not have been dug by one man and believe they may date back centuries.
Tour guide Margaretanne Dugan said: "The Covenanters may have hid down here. They signed the National Covenant 1638, so it would have been ideal for secret religious worship.
"We also have some Masonic marks on the table tops, so perhaps it was a gentlemen's secret club."
And in keeping with Edinburgh's traditions, there are even claims that the passageways may be haunted.
Ms Dugan said: "One of our trustees asked the question: what lies beyond the rubble in this room? Well, I kid you not, when we played back the recording you can hear a voice saying: [whispers] never mind."
Source: STV News
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