With some have become famous tourist destinations, others have been long forgotten and all have been left uninhabited for years.
Drum Street in Gilmerton is home to the subterranean chambers of a remarkable cave thought to have been inhabited up to 300 years ago. The cave is a 40-feet long passage with a series of unusual rooms and passages.
The Innocent line was a horse-drawn railway connecting St Leonards and Dalkeith. Completed in 1831, it was Edinburghs debut railway, and its tunnel is one of the oldest in the United Kingdom.
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Construction on the Scotland Street Tunnel began during the early 1840s but was abandoned in 1868 after only 21 years of operation. A narrow ventilation pipe is now the only visible indication of its existence at its southern end.
Constructed in 1875 as part of the Alnwickhill waterworks, the vaulted cathedral-like space served as a 15-million gallon tank, storing the citys water.
Waverley vaults were built during a 1.5 million redevelopment and expansion of Waverley Station by the North British Railway Company in the mid-1890s.
The Real Mary King's Close is now a popular tourist attraction that tells the tales of the densely-inhabited close, many of which are ghostly and gruesome.
Between the arches of South Bridge exists a system of vaults, which were used to house taverns, cobblers, a distillery and other trades but were abandoned due to the lack of light and sanitation.
Buried 100 feet beneath a graffiti-laden structure on Corstorphine Hill lies a chilling remnant of the Cold War: a secret bunker equipped to house hundreds of state and military officials in the event of nuclear fallout.
One of Edinburgh's most haunted sites, tours of the Blair Street Vaults are available and not for the faint hearted.