We know little about Minoan religion, but it is clear that religion was an important aspect of Minoan life. There were only minor male deities; the goddesses were supreme. It is unclear whether the goddesses represent two or three goddesses or only one with different aspects. There are several distinguishable goddess identities - a goddess associated with animals, sometimes called the Mistress of the Animals, a snake goddess who typically has snakes wrapped around her arms, a household goddess, and others. Scholars believe that these identities eventually found their way into the Greek pantheon as Hera, Artemis and other female gods.

This detail from the Sarcophagus of Ayia Triada show a ritual bull sacrifice

The society was matrilineal, that is they traced their descent through the female line, unlike the patrilineal societies which dominated bronze age Europe. Surprisingly for a bronze age urban culture, women retained their power in religion and in society.

The priestesses were female, and Minoan religion was matriarchal with an all-powerful mother goddess. This is true of many very ancient religions. With the advent of urbanization around the world matriarchal religions were gradually replaced by patriarchal ones, just as the Greek patriarchal religion (the pantheon led by Zeus) eventually replaced the Minoan matriarchal religon. The Minoans did not bring about this change, however. The Minoan matriarchal religion existed side by side with the Mycenaean patriarchal religion of mainland Greece until the Minoans disappeared, conquered by the Mycenaeans.

Many outdoor nature shrines have been discovered some in caves, others on hill tops. Some tree shrines enclosed growing trees. There are depictions of women dancing around the trees, shaking the branches. Household shrines and shrines at tombs have also been discovered. Artifacts indicate that religious practice involved dance, procession, sacrifice and offerings.