The roots of the MahaSiddha Tradition emerged from the indigenous Tantric spirituality of ancient India. Historically it is said that the dynamic healer and spiritual leader first known as Shiva was the first teacher of Tantra. Though it is clear that Shiva was the original Yogi who wore the cremation ground ornaments, carried the damaru and practiced Tantra, there is much disagreement between traditions as to how elements of Indian Tantra came to be intermingled with Buddhism. It is clear that it did happen; Indian Tantra was a crucial factor in the development of Buddhist Tantra.

Non-buddhist origins of Yoga and Tantra eventually converged with the Buddhist teachings to bring forth the early seeds of Tantric Buddhism. Indian Tantras continuously influenced Tibet and Tibetan Buddhism by way of wandering Yogins who were not organized, nor concerned with spreading any particular religion. Instead, they traveled sharing what they had practiced and experienced whether or not it was "Tantric" or "Buddhist." Their non-sectarian spirit was very much intact in the MahaSiddha's lives and teachings. The sheer variety and non-uniformity of their religious, cultural and social backgrounds reveals the wide applicability of their spirituality.

In a traditional story, Tantric Buddhism was born after the wild form of Shiva, called Rudra, passed through a stage where his ego became horribly ugly and inflated. He was behaving so awfully that the Primordial Wisdom Buddhas intervened. Out of compassion, they gave him a transmission of realization beyond "self," which freed him from egoism. From that moment, though Rudra appeared as he was before, he had now realized emptiness of self and the Tantras of Buddhism were manifest. The origins of the MahaSiddha Tradition can be traced back to these and other indigenous Indian realized beings who expressed non-dual spirituality in it's primitive form.

As it emerged the essential aspect of the Indian Tantras was the view that life was intrinsically pure and that subjective conceptions of good and bad are often confused. The various lineages of Tantra, including the MahaSiddha Tradition, shared methods for transforming mind from confusion to wisdom in order to return to an intrinsically pure, awake state. A variety of teachings, religions and traditions emerged out of the early Tantras of India. The Tantric practices inherited by the MahaSiddhas were body-positive and practiced by females and males.

Shakyamuni Buddha gave Tantric teachings in the "third turning of the wheel of the dharma" around 400 b.c.e.. He explained that these teachings would not be fully articulated and widely shared until the birth of the Tantric Buddha (Padmasambhava). It was not until around 400-500 c.e. that the Tantras actually developed into a systemitized body teachings with written texts and various schools developing and spreading it. It was at approximately 800 c.e. that the Tantras bore mature fruit in Padmasambhava's life and teachings. As the MahaSiddha Tradition developed it became "Vajrayana," which evolved into various forms in Tibet. The Inner Tantra of the MahaSiddhas is Vajrayana stripped of cultural trappings.

In 1999, Kali Ma founded MahaSiddha Dharma, a non-profit organization to express, make visible and make accessible the essential spiritual style of the MahaSiddhas, whose lineage Kali Ma received as a young woman.