The Greek Speleological Society has recorded over 3.000 caves in Crete. Not only astounding examples of nature's talent for interior decoration, many of them are also of great scientific value, being of archaeological, paleontological and historical interest.
Man used caves as places of workship, as well as dwellings from the Paleolithic era on.

The Minoans began the custom of workshipping their gods in small palatial or house shrines, in sacred caves and in shrines built on mountain peaks and the tops of hills.
The cave of Sentoni Zoniana , This is Crete's richest cave in terms of natural decoration. It lies in the district of Rethimno, 13 km. west of Anogia and 1 km. from the village of Zoniana at an altitude of 800 m.
The Diktaian Cave (Dikteon Andron) . The legendary birthplace of Zeus, this can be reached by going to the outskirts of the village of Psihro (48 km east of Iraklio and 52 km. west of Agios Nikolaos), where is a path ascending to it. Significant archaeological finds indicate that the cave was long a place of cult worship. One can go from the village to the cave on foot or by mule or donkey, which can be rented from the locals. The descent into the fascinating cave demands some caution. Stalagtites of various shapes adorn the lower cave.
The Idaian Cave (Ideon Andron). 20 km south of Anogia on the upland plain of Nidas, on Mount Psiloritis, lies this sacred cave, where according to mythology, rhea hid the baby Zeus from the murderous Kronos. Cult objects have been found here, along with statues and bronze shields and other finds now on display in the Iraklio Archaeological Museum
The Cave of Eileithyia (Ilithiia) . This cave was used for cult rituals from the Neolithic era up to the 5th century B.C. Lying 1 km south of Amnissos, it was sacred to Eileithyia, the goddess of childbirth. Archaeological investigations here uncovered idols of woman in the act of giving birth, nursing or praying, figures of animals, neolithic shells and tools.
The cave of Ag. Paraskevi Skotinou, 22 km from Iraklio. This very interesting cave used for cult worship both in antiquity and during the Christian era.
The Kamares Cave. Northeast of the Village of Kamares (57 km from Iraklio) lies the cave of Kamares, established during the Minoan period as a sacred spot, possibly dedicated to the worship of the goddess Eileithyia. The wonderful Kamares vases, on display in the Archaeological Museum of Iraklio were found here. Visiting the cave entails a 4-hour walk from the village.
The Gerani cave of Rethimno 6km. From Rethimno, this is a cave of prehistoric, paleontogical and archaeological interest. Find from this cave may be seen in the Rethimno archaeological museum.
The Melidoni Cave. 3 km. From the village of Melidoni (26 km east of Rethimno), this was used for cult worship during the Neolithic, Minoan and Archaic periods.
The cave of Aghios Antonios near the village of Patsos also represents a place of dedication as has been proved by archaeological research. It was used as an important centre of worship from the Late Minoan up until the Roman period. An inscription that was found in the cave testifies that Hermes Kraneos was worshipped here. The church in the interior of the cave is dedicated to Aghios Antonios, the patron of the children. The cave is open to visitors.
CAVE OF MILATOS
In the area, which is commonly known
as The Cave of Rapa, and more
generally as The Cave of Milatos,
it is located East of Milatos.
Its height is 155m. The cave has
eight small and larger entrances,
covering a space of 40m with three
different levels. The cave of Milatos
is well known because of the drama
that occurred there in February
of 1823. The infamous Hasan Pasas,
having destroyed and devastated
Lasithi at the beginning of 1823,
took action in Mirabello. The citizens
foreseeing their fate went to hide in
the caves. The residents of Vrahasi
went to the Cave of Peristera, and
those from Upper Mirabello went to
the Cave of Milatos. Hasan Pasas
sent the Albanian deputy-general
Husain Vei with 5000 soldiers to attack the cave. The local military guards tried to restrain Husain, and caused him considerable damage, but finally the cave was surrounded. The 150 defenders fought bravely and killed many of the attacking force. This horrendous drama lasted from the third to the fifteenth of February, 1823.The hostages began to experience the tortures of thirst and hunger. The smell of dead bodies was
terrible. The pressure from the attackers was increasing.
Cannons were brought in and they bombarded the entrance to
the cave from the opposite heights. The hostages were suffering
patiently. They expected help from the outside. In fact, 2500
soldiers came to help. The numbers of soldiers of Hasas Pasa and
their cannon power was overwhelming. The Turks called upon the
prisoners to surrender, swearing that they would not harm them,
but the Christians were unable to believe their guarantees.
Finally, their needs forced them to make an exit. Initially the
warriors ventured out. The first thirty who came out were
mercilessly slaughtered by the Turks. This was followed by the
pursuit and massacre of women and children. Those who were
captured were tied up with ropes and chains and driven to
Neapolis. The older people were transferred to a place called
Grampelis. There the Turkish cavalry trampled them to death.
They beheaded them and made a pyramid of the heads as a trophy, and the women and children were sold as slaves. The infants were completely butchered. Eighteen priests were killed or burned alive. This is how the terrible drama of the Caves of Milatos ended.
ATZIGKANOSPILIOS
The opening of the cave is found at the base of an isolated strata of calcareous rock, 10k north-east of the village of Andrianos of Mirabello, in Notiko Halambouti in the expansive area of Koukistres. It has four antechambers and five chambers. The first chamber is larger than the others. The full length of the cave is 48m, but its entire course is almost 100m.
THERGIOSPILIOS
Located at a place called Hiloftes-Thergio, east of the village of Kavousi of Ierapetra. The height is 50m. Towards the north east there is a sheer cliff called "The Sword of Homata" where one can see graphic layers of Filitis and slabs of calcareous rock-crystal and Dolmadic rock. The rock in the area of the caves is Dolmadic type from the Tertiary period. Above the cave there is a small intrusion of aluminum, and the local people refer to it as "Blade " or "Agolifa".
MEGALO KATOFIGI
The cave is arrived at by following a steep incline north-west of the village of Tourtouroi (now called St. George), Sitia. Its height is 450m. It occurs within Jurassic Limestone rock. It is richly decorated. The entire course inside of the cave is almost 100m.
OKSO LATSIDI
Located in Patelia, 10k north west of the village of Sitanos, Sitia. Its height is 610m. It occurs in Jurassic Limestone. Further north there are Pre-tertiary Filites, and north west and north east there are small masses of Dolmadic rock from the Tertiary period. Only 50m of the cave had been explored by the locals. Then, P. Faure explored the whole cave on the 26th of July, 1967. Some days later, it was mapped and studied by El. Platakis and Io. Tsiftetakis. The entire length is 360 m.
CAVE PELEKITA OR SIKIAS SPILIOS
Located north east of the small village of Kato Zakros. The cave can be reached by travelling one hour from Kato Zakros, or from the beach of the village by using mechanised boats and then making an ascent. The height at the entrance is 105m. The whole area is commonly known as Belekita, which name is derived from the quarry, which is below the cave, close to the sea, from which stones have been extracted. The other name "Sykias Spilios" was given to the cave because of the location of a large fig tree at the entrance. Under the cave one can see the sea as if viewing it from a plane.
Peristeras
Located approximately 2.3 km east of the village of Karidi, Sitia, below Platyvolo or Peristeras. The height at the entrance is 540m. The village of Karidi is built on classified sedentary rock of the Pre-Tertiary Period, that intrudes from west to east through the Jurassic Limestone in which is the opening of the cave. It is classified as an abyss-cave. Beyond the entrance of the cave, due to the corrosive action of the water, a part of the roof fell in and made an archway at the entrance of the cave, the dimensions of which are 48 x 26m, with a depth of 17-25m. The entire course of the interior of the cave is approximately 170m.
Agios Mamas Cave
The road continues beyond the church and climbs up out of the valley. On the mountainside is a cave with a small church, called Agios Mamas, inside it. On the feast day of the church, boiled meat is eaten. It is thought that this custom is a direct descendant from the animal sacrifice of the ancient god Pan. Evidence of animal sacrifice have been found in the cave.
Hermits' Cave of Saint John
This cave is called Hermits' Cave of Saint John, as it is said that the saint has lived here until his death. The legend tells, Saint John had to flee from the Middle East with 98 friends and came to this cave. The cave is smaller than nearby Gouverneto Cave. It is not clear to us where his friend remained, but obviously not in the rather small cave.
The main sight of the cave is a formation resembling (and used as) an altar. The saint is said to have slept on this formation. It is located on the left wall of the last chamber.
Another legend tells, St. John was killed by the bullet (or the arrow) of a hunter, while he was collecting herbs. The hunter thought he was a bear because of his fur clothes.
The trail leads down into the gorge to Katholiko monastery. Reckon at least half an hour for the way down and one hour for the way back uphill. Be sure to take enough water with you.
There is also a cave church Iero Spileo (cave church), which is part of the Katholiko monastery. The facade of the church is buit in Venetian style. A roomy passage ends in a large chamber called The Saint's Bedroom. The saint being St John the Hermit who is reputed to have lived in this cave and after whom this cave is sometimes called. In the left hand wall there is a natural shelf of stalagmite which is called The Altar. Every Autumn a memorial service is held here.
Matala Caves
The Matala Caves are artificial caves in sandstone, cut by man since prehistoric times. They are located above the cove of Matala, on the southern coast of Crete. The face of the cliff is spreckeled with caves, many of them can easily be visited.
Although of great archaeological interest, the caves became famous in the 1960s, because they were used as a place to live by international hippies. Obviously the local administration was not happy with this sort of squatting, but they did little against it. It is said that even famosu people of the 1960s and 1970s, like Cat Stevens and Joni Mitchell stayed at the caves for some times. However, finally little remained of the enthusiastic start and the cave were becoming a home to criminals and drug dealers. At least thats what the gouvernment said when they finally closed the caves and cleaned them. Today nobody lives at the caves, but again it is possible to visit them freely.