In Tibetan Buddhism, the Three Jewels and Three Roots are supports in which a Buddhist takes refuge by means of a prayer or recitation at the beginning of the day or of a practice session. The Three Jewels are the first and the Three Roots are the second set of three Tibetan Buddhist refuge formulations, the Outer, Inner and Secret forms of the Three Jewels. The 'Outer' form is the 'Triple Gem', (Sanskrit:triratna), the 'Inner' is the Three Roots and the 'Secret' form is the 'Three Bodies' or trikāya of a Buddha.
These are: the Buddha, the fully enlightened one the Dharma, the teachings expounded by the Buddha the Saṅgha, the monastic order of Buddhism that practice the Dharma the Lama (Sanskrit: guru) is the 'root of blessing' or 'root of grace' the Yidam (Sanskrit: ishtadevata) is the 'root of methods' or 'root of accomplishments' the Dakini or Dharmapala is the 'root of activity' or 'root of protection'.
The additional refuge formulations are employed by those undertaking deity yoga and other tantric practices within the Tibetan Buddhist Vajrayana tradition as a means of recognizing the universality of Buddha Nature. The Three Roots are commonly mentioned in the Nyingma and Kagyu literature of Tibetan Buddhism. Unlike most aspects of Tibetan Buddhism, which originated in India, the Three Roots may be an original Tibetan formulation from the time of Padmasambhava.
Individual Jewels
Buddha
Lord Buddha is the Enlightened One who discovered the Ultimate Path to release clinging and craving and liberation from the cycle of birth and rebirth.
Dharma
For practising Buddhists, references to "Dharma" (Dhamma in Pali) particularly as "the dharma", generally means the teachings of the Buddha, commonly known throughout the East as Buddhadharma. It includes especially the discourses on the fundamental principles (such as the Four Noble Truths and the Noble Eightfold Path), as opposed to the parables and to the poems.
Saṅgha
The Saṅgha is the third of the Three Refuges. Common over all schools is that the āryasaṅgha is the foremost form of this third jewel. As for recognizable current-life forms, the interpretation of what is the Jewel depends on how a school defines Saṅgha. E.g. for many schools, monastic life is considered to provide the safest and most suitable environment for advancing toward enlightenment and liberation due to the temptations and vicissitudes of life in the world.
Vajrayana and Dzogchen formulations
Dilgo Khyentse, head of the Nyingma school of Tibetan Buddhism until his death in 1991, explained the twilight language correspondences and meaning of the Outer, Inner and Secret aspects of the Three Jewels:
The Three Roots formulation also fits into the framework of the Trikāya ('three bodies') of a Buddha where they are seen as equating to the following forms: the protector is the body, the yidam is the Speech and the lama is the mind. According to the Handbook of Tibetan Buddhist Symbols:
Pabongkhapa Déchen Nyingpo also identifies the seed syllables corresponding to the Three Vajras as: a white om (enlightened body), a red ah (enlightened speech) and a blue hum (enlightened mind).
Three refuge motivation levels are: suffering rebirth's fear motivates with the idea of happiness, knowing rebirth won’t bring freedoms motivates attaining nirvana, while seeing other’s suffering motivates establishing them all in Buddhahood.
Happiness is temporary, lifetimes are impermanent and ultimately refuge is taken until reaching unsurpassable awakening.
Individual Roots
Lama
In the Theravada Buddhist tradition, the teacher is a valued and honoured mentor worthy of great respect and a source of inspiration on the path to Enlightenment. In the Tibetan tradition, however, the teacher is viewed as the very root of spiritual realization and the basis of the entire path. Without the teacher, it is asserted, there can be no experience or insight. The lama is seen as Buddha. In Tibetan texts, emphasis is placed upon praising the virtues of the lama. Tantric teachings include generating visualisations of the lama and making offerings praising the lama. The lama becomes known as the vajra (literally "diamond") guru, the one who is the source of initiation into the tantric deity. The disciple is asked to enter into a series of vows and commitments that ensure the maintenance of the spiritual link with the understanding that to break this link is a serious downfall.